CHAPTER 4 Operation Codes

This section is intended as a reference guide for the use of the operation codes. Unless otherwise specified, a zero in any opcode argument specifies the default value, if there is a default. Also, unless otherwise specified, the default is a reasonable value to choose if you do not have a good reason to select a different value.

File Reading and Writing:

WRIT - WRITe a Structure

TRED - Temporary file REaD

TOPN - Temporary file OPeN

filename.dat

filename.out

DEBG 1

READ

TOPN 100

BGIN

TRED

WRIT

END

The above command file will open the filename.dat structure file and the filename.tmp temporary file, read in the first 100 coordinate sets from the temporary file and write the corresponding structures to the output structure file, filename.out. Arg1 of TOPN is the number of structures to be read from the temporary file. See the end of the failed job log file to find this number; however, be aware that the last structure in the .tmp file may be corrupted, depending on the nature of the failure of the previous job.

If this operation is to be used to recover structures from a run which used the SUBS command, then the SUBS commands in the original run must be included immediately after the READ command in the command list above.

A file having the same name as the .dat file but with an .m2 suffix conveys structural information to MacroModel, which displays it in the MacroModel 3D GLX or MacroModel 2D window. For energy minimization or molecular dynamics, the structure written is the latest one encountered during the procedure. During conformational searching, the global minimum found so far is written; thus, interactive monitoring of conformational search does not display much action.

The writing of MacroModel structural files can slow BatchMin down tremendously, especially on NFS-mounted filesystems. Thus, lowering the frequency of writing, or eliminating it entirely by removing the MMOD command, is worth considering for long jobs.

arg1 Frequency of writing to the .m2 structural data file (default = 1)

1      BatchMin writes to the .m2 file as frequently as it can for real-time monitoring. For long jobs, however, this slows BatchMin execution.

n      Write the file only 1/n times as frequently as it otherwise would. Thus, arg1=10 would update the .m2 file 1/10 as frequently as the maximum rate.

0      No recoloring will be done.

1      Atoms will be recolored by energy gradient, an index of strain. A color scheme is used that follows the spectrum, where the red atoms indicate the most highly strained region of the molecule and the blue colors indicate the most relaxed regions.

The force-field files we supply have names fieldname.fld, where fieldname is one of: mm2, mm3, amber, amber94, oplsa or f10. BatchMin first looks in the local directory for the specified force-field file and, if it is not found there, looks in the directory given in the BATCH_ROOT environment variable. Before looking for fieldname.fld, however, BatchMin looks locally for file called filename.fieldname; for example, my_job.amber. Under certain circumstances, other processes preparing jobs for running by BatchMin use this convention.

arg1 Force field

1      MM2*. Allinger's 1987 parameter set with many additions. Used for simple organics. Differs from the authentic field by use of a Coulomb's law treatment of electrostatics and torsional barrier treatment of conjugation. Key references: J. Am. Chem. Soc., 99, 8127 (1977); ACS Monograph 177, "Molecular Mechanics"

2      MM3*. Allinger's 1990 parameter set with additions. Used for simple organics. Differs from the authentic field by use of a Coulomb's law treatment of electrostatics and torsional barrier treatment of conjugation. Key reference: J. Am. Chem. Soc., 111, 8551 (1989).

3       AMBER*. Kollman's united atom and all atom fields with additional parameters for organic functionality. Used primarily for biopolymers. Key reference: J.Am.Chem.Soc., 106, 765 (1984); J.Comp.Chem., 7, 230 (1986).

4      AMBER94. Kollman's 1994 version of AMBER, Amber4.1. Key reference: Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A., J. Am. Chem. Soc. 1995, 117, 5179.

5      OPLSA*. Jorgensen's nonbonded parameter set + AMBER bonded functions for liquid simulations. Used primarily for peptides. Best for relatively rigid molecules, because the torsional params have not been optimized to reproduce conformational energy differences. Key reference: J.Am.Chem.Soc., 110, 1657 (1988).

10      MMFF94 and MMFF94s. See also the description of arg4 of this command. Key references: T. A. Halgren, J. Comput. Chem., 1996, 17, 490-519, 520-552, 553-586, 587-615, 616-641 and J. Comput Chem., 1999, 20, 720-729, 730-748.

11      OPLS-AA. This force-field, developed by Professor W. Jorgenson of Yale University, is probably the best one available for condensed-phase simulations of peptides. In collaboration with Professor Jorgensens laboratory, we are extending the parameterization to broader classes of drug-like molecules. See current release notes for details of the latest parameterization. Key reference: Jorgensen, W. L.; Maxwell, D.S.; Tirado-Rives, J. Am Chem. Soc. 1996, 118, 11225-11236. A value of 10 or more for arg1 encodes a force-field whose parameters are obtained from a coprocess interacting with BatchMin using the BMFF mechanism. See Appendix 5 for details. The force-field filnename used in this case is fnn.fld, where nn stands for the number; thus, the MMFF force-field file is f10.fld.

0      Default. Uses dielectric treatment encoded within force field file unless solvation model 3 is used (see SOLV command), in which case the constant dielectric treatment is used.

All our force fields are supplied, by default, with constant dielectric electrostatics. Prior to MacroModel 6.0 , AMBER*, MM2 and MM3 used distance-dependent dielectric constant by default.

-1      Turns Coulombic molecular electrostatics off.

1       Gives constant dielectric electrostatics.

2       Gives distance-dependent dielectric electrostatics.

0      uses equation selected in force field file (default).

1      turns off explicit 10,12 hydrogen bonding function and uses 6,12 Lennard Jones instead.

2      gives explicit 10,12 hydrogen bonding function.

arg5 Molecular dielectric constant

FFOP - Force FieLD OPtion Selection

arg1 ALT number

arg2 ALT selection

): 41	*: 42	+: 43	,: 44	-: 45	.: 46	/: 47	0: 48	1: 49	2: 50
3: 51	4: 52	5: 53	6: 54	7: 55	8: 56	9: 57	:: 58	;: 59	<: 60
=: 61	>: 62	?: 63	@: 64	A: 65	B: 66	C: 67	D: 68	E: 69	F: 70
G: 71	H: 72	I: 73	J: 74	K: 75	L: 76	M: 77	N: 78	O: 79	P: 80
Q: 81	R: 82	S: 83	T: 84	U: 85	V: 86	W: 87	X: 88	Y: 89	Z: 90
[: 91	: 92	]: 93	^: 94	_: 95	`: 96	a: 97	b: 98	c: 99	d:100
e:101	f:102	g:103	h:104	i:105	j:106	k:107	l:108	m:109	n:110
o:111	p:112	q:113	r:114	s:115	t:116	u:117	v:118	w:119	x:120
y:121	z:122	{:123	|:124	}:125	~:126

EXNB - Use EXtended noNBonded cutoffs.

Extended cutoff distances are, by default, 8Å in vdW, 20Å in charge/charge electrostatics. Standard defaults in the absence of this command are 7Å for vdW and 12Å for charge/charge electrostatics. Other cutoffs may be selected by adding values for arg5-8. Calculations dealing with ions should use the EXNB option.

Large distance values for cutoffs generally slow calculations but often make convergence smoother. Occasional problems with energies and gradients which appear to increase upon repeated minimizations may usually be solved by using long van der Waals and electrostatic cutoff distances. The native MM2/MM3 and MMFF programs use complete pair lists (no cutoffs) for van-der-Waals and electrostatic interactions.

arg 1 Long-range derivative update interval

1      The constant long-range derivative option is turned off, and the entire pair list is used in the evaluation of nonbonded derivatives.

2      All nonbonded pairs are put on the pair list, and the pairlist is never updated. Long-range derivatives are used.

3      Like a combination of 1 and 2: all nonbonded pairs are put on the pairlist, the pairlist is never updated, and the entire pairlist is used in each evaluation of nonbonded derivatives.

arg5 van der Waals cutoff

arg8 Fmm cutoff

Regardless of the user's setting of arg8, the program will not allow the Fmm cutoff to exceed the larger of the van-der-Waals and the electrostatic cutoff.

0 Default: 8.0 Å

>0      Interpreted as Å.

<0      Interpreted as 0.

arg 5 CutsFm cutoff

0      8.0 Angstroms(default).

n      n Angstroms.

Solvation model 1 is involved explicit solvent, and is no longer supported.

Models 2 and 3 read the appropriate solvent file named solvent_name.slv . water.slv and chcl3.slv are available. BatchMin first looks in the local directory for the .slv file and, if it is not found there, looks in the BATCH_ROOT directory.

Solvent model 2 (arg1 = 2) is purely a surface-area-based model. We recommend model 3 for all computations where solvation energies are desired. Model 2 operates as described in Hasel, Hendrickson and Still, Tetrahedron Computer Methodology, 1, 103, 1988. See also Ooi, Oobatake, Nemethy and Scheraga, PNAS, 84, 3086 (1987) for the parameter set given in water.slv. Solvent model 3 provides a volume-based continuum model (the GB/SA model) for the electrostatic (polarization) component. See Still, Tempczyk, Hawley and Hendrickson, J. Am. Chem. Soc., 112, 6127 (1990).

Using model 3, molecular electrostatics should be carried out with a constant dielectric treatment and a low molecular dielectric constant (e.g. 1.0). Constant dielectric electrostatics will be set automatically whenever solvent model 3 is used regardless of the default electrostatic equation selection in the force field file. EXNB should also be used with solvent model 3.

Calculations with solvation use periodically updated constant area and/or polarization derivatives to speed the calculation. Default update frequencies are given below. These frequencies can be changed via arg3 and arg4. If difficulties in achieving low gradients are found or if dynamics in solvent is unstable, reduce these numbers (e.g. to 2). Energy minimizations and molecular dynamics simulations using continuum solvation models 2 and 3 run approximately 1/2-1/4 the rate of in vacuo calculations.

BatchMin carries out energy minimizations with an analytical, approximate function for surface areas. Thus, intermediate energies reflect the approximate function. The final energies reported, however, use an accurate numerical function. Thus, intermediate and final energies will differ.

arg1 Solvation model

2      Total solvation based on approximate solvent accessible surface areas (Scheraga's parameters).

3      GB/SA Solvation Model. Cavity and Van der Waals components from approximate solvent accessible surface areas, and electrostatic (polarization) component from GB mode. See discussion of effective Born radii calculation in the article:. J. Am. Chem. Soc., 112, 6127 (1990). This is the best solvent model to use.

1      WATER (models 2 and 3)

5      CHCL₃ (model 3)

Used in models 2 and 3. (Default: 25 (new value in MacroModel 6.5) for PRCG, SD, and OSVM minimization modes and molecular dynamics, and 1 for FMNR and TNCG. Set to 1 or 2 for problem minimizations using SD, PRCG or OSVM; the default value cannot be overridden for FMNR and TNCG.

arg4 Solvent polarization reset frequency

arg5 Minimum solvent/solute distance

arg6 Flat-bottom positional constraint force constant

arg7 Half-width of flat-bottomed positional constraint

arg8 Maximum distance from solute centroid

CHGF - CHarGe File

arg1 Source of charges

0      use atomic charges from input structure file (default)

-1      turn CHGF off

The only place in which this facility is currently used is in the treatment of sp3 CH_n groups. When charges are assigned by the force-field, then, for the purpose of GB calculations only, charges on hydrogens in such a group will be added to the charge on the carbon, and the entire group will be treated as a united atom.

When reading an input file, the values in the first charge column will be used for Coulombic calculations and those in the second charge column will be used for GB. This argument allows control over the uniting of CH_n groups in this situation.

0      (Default.) If all H's of an all-atom CH_n group have zero charge, unite the group for GB calculations; otherwise, treat these H's explicitly. If a file is written out containing force-field charges, this default recaptures the force-field behavior should the file subsequently be read in with CHGF in effect.

1      Never unite all-atom sp3 CH_n groups for GB.

2      Always unite all-atom sp3 CH_n groups in GB. This allows a structure with equal charge columns to be read in with CHGF and for the default behavior to be embodied in the output; that is, the output will be suitable for reading with CHGF arg2=0.

arg1 Number of passes through the BGIN/END loop

0      Continue looping until some other termination condition - such as an end-of-file - is encountered.

>1      Execute this number of passes through the loop.

0      Exit the program.

1      Skip to the top of the next iteration. This option is useful if one is minimizing many diverse structures, some of which may lack appropriate parameters.

2      Attempt to continue execution.

REST - RESTart

RWND - ReWiND file

arg1 Which file is to be rewound

0      The current output (.out) file.

1      The current input (.dat) file.

0      Discard; at the end of program execution, there will be a single output file, typically named filename.out, that contains only the output generated following the last RWND command.

1      Keep intermediate output in separate files, typically named filename.ou1, filename.ou2, etc. The final output appears in filename.out.

2      Keep all intermediate output, together with final output, in a single file, typically named filename.out.

arg1 Control

0      Hydrogens added to all atoms of structure

1      Hydrogens added to all non-carbon atoms of structure