geninput.pl

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Description

Generates an input file for MONSSTER. Available parameters and their default values are shown in the table below. The values can be overwritten by specifying the parameter name and the new value with -par

Key	Explanation	Default
random	random seed	random value
ncycle	cycles/temp. step	20
icycle	MC moves/cycle	50
tsteps	temperature steps	10
resmin	first fragment residue (fixed template)	0
resmax	last fragment residue (fixed template)	0
temp	temperature range	2.5:1.0
softcore	soft core radius for large residues	4.0
central	centrosymmetric potential scaling	0.25
stiff	general stiffness potential scaling	1.25
pair	pair potential scaling	1.0
kdcore	hydrophobic core potential scaling	0.35
hbond	H-bond cooperativity potential scaling	-0.3
short	short range potential scaling	0.5
burial	burial potential scaling	1.0
multibody	multi body potential scaling	0.5
threebody	3 body potential scaling	0.25

Distance constraints between residues (e.g. if disulfide linkages are known) may be specified using -d with a force constant and a list of residue pairs as parameters. A MONSSTER sequence file may be given with -seq for translating the residue numbering accordingly.

Options

-help 

usage information

Examples

geninput.pl
generates the default MONSSTER input file

520735 20 50 10
0 0
2.50 1.00 4.000 0.250
1.250 1.000 0.350 -0.300 0.500
1.000 0.500 0.250
0 0.0
0
0
0
0

geninput.pl -par ncycle=50,stiff=0.1 -d 5.0 10:34=19:26
generates a MONSSTER input file iwth 50 cycles per time step and a modified scaling factor for the general stiffness potential term. In addition sidechain restraints are specified between residues 10 and 34 as well as 19 and 26.

657610 50 50 10
0 0
2.50 1.00 4.000 0.250
0.100 1.000 0.350 -0.300 0.500
1.000 0.500 0.250
2 5.000000
10 34
19 26
0
0

...