The usage of the program is as follow
exttrjcrds exttrjcrds.in
where exttrjcrds.in is a textfile controlling the behaviour of the program.
The code is written in Fortran95 and located locally in /away/bio/Amber/ExtTrjCrds
Samuel Genheden, 2012
The control file contains values of variables determining the execution of ExtTrjCrds. Each variable name starts with an ampersand (&) and the rows that follow the variable name sets the variable and associated variables. Currently, the following variables can be set:
$nprot - the number of protein atoms found in the $protfil-files. Can be set to 0, which is the default. In this situation all protein atoms are written out, and truncated snapshots will not be written by setting $wrttr to 0.
$nlig - the number of ligands atoms found in the $ligfil-files. Can be set to 0, but only if $reccalc is set to 1, i.e., it is trajectories of an unbound protein.
$nwat - the number of water molecules to write in the output snapshots. Default = 0.
$nsel - only write out snapshots which have this specific number of water molecules in the binding site. Default = -1, i.e., write out all snapshots.
$prmtop - an Amber prmtop-file that was used to generate the MD trajectories.
$crds - the MD trajectories. The first line after the variable name should be an integer, specifying the number of trajectories to process, n. The next n lines contains two, three, or four columns. In all cases the first column should specify the name of the trajectory-file. If two columns are given, the second column should specify the last snapshot to process and the first and frequency is set to 1. If three columns are given, the second and third column should specify the first and last snapshot to process, respectively and frequency is set to 1. If four columns are given, the last column is the frequency of processing.
$protfil - a file that on each line should have an atom number, and these protein atoms are written to the output snapshots. If $wrttr is 1, these protein atoms will be written out to the truncated snapshots, and all protein atoms are written out to the other snapshots.
$ligfil - a file that on each line should have an atom number, and these ligand atoms are writen to the output snapshots.
$reffil - a pdb-file that is used a reference when finding the binding site water molecules. Only need to be set if $explicit is turned on.
$reflig - determines which atoms in the reference pdb-file that are consider to be the reference ligand. Two integers must be given, the first and the last ligand atom, separated by space. Only need to be set if $explicit is turned on.
$siterad - the radius that determines the extent of the binding site. Any water molecule within at least this radius from any reference-ligand atom is considered to be a binding site water molecule. Default = 3 A.
$fitrad - a radius that determine which residues that are used to superpose the snapshots onto the reference pdb-file. All residues with at least one atom within this radius from any reference-ligand atoms is used in the superpositioning. Does not have be set, default = 10 A.
$prefix - the prefix that is appended to the start of all output-snapshot files. The complex snapshots will be named $prefix_com.crd.X, where X is an ordinal number, the receptor snapshots will be named $prefix_rec.crd.X and the ligand snapshots will be named $prefix_lig.crd.X.
$reccalc - can be either 1 or 0 and turns on/off receptor calculation. If it is on (1), then only snapshot will be written for the receptor. Turning this on, turns automatically $wrtcom and $wrtlig off. Default = 0 (off)
$explicit - can be either 1 or 0 and turns on/off explicit water calculation. This means that each snapshot is superposed on a reference pdb-file and the number of water molecules in the binding site is determined. If this is turn on, one must specify a reference pdb-file ($reffil) and a reference ligand ($reflig). Also if this is turned on, only the oxygen and the hydrogen atoms of the water molecules will be written out, i.e., extra point charges in e.g. TIP4PEw will be ignored. Default = 0 (off).
$wrtcom - can be either 1 or 0 and turns on/off writing out complex snapshots. Default = 1 (on)
$wrtlig - can be either 1 or 0 and turns on/off writing out ligand snapshots. Default = 1 (on)
$wrttr - can be either 1 or 0 and turns on/off writing out truncated snapshots for normal mode calculations. Default = 0 (off)
$comasrec - can be either 1 or 0 and turns on/off writing out complex snapshots under the name of receptor snapshots, i.e., the receptor snapshots will actually contain ligand coordinates. Default = 0 (off)
By combining different input variables the snapshots for many situations can be created.
To create standard snapshots and truncated snapshots for standard one average MM/GBSA. prot.atoms specify the protein atoms to print out in the truncated snapshots. The 108 water molecules will only be printed in the truncated snapshots.
$nprot
1809
$nlig
31
$nwat
108
$prmtop
ferr-l01.prm
$protfil
prot.atoms
$ligfil
lig.atoms
$crds
1
r1_cent.mdcrd 1 40
$prefix
l01
$wrttr
1
Same as above, but the receptor snapshots will also include the ligand atoms, which could be interesting if one would like to prevent the cavity to be filled with continuum water.
$nprot
1809
$nlig
31
$nwat
108
$prmtop
ferr-l01.prm
$protfil
prot.atoms
$ligfil
lig.atoms
$crds
1
r1_cent.mdcrd 1 40
$prefix
l01
$wrttr
1
$comasrec
1
To create snapshots for an apo protein, i.e., a trajectory without any ligand, as in a three-average MM/GBSA.
$nprot
1809
$nwat
108
$prmtop
apo.prm
$protfil
prot.atoms
$crds
1
r1_cent.mdcrd 1 40
$prefix
ferr
$wrttr
1
$reccalc
1
To create regular snapshots but with 10 water molecules. The 10 water molecules would be found by superposing the snapshots onto ref.pdb and looking for water molecules within 4 A of the atoms 2455 to 2476.
$nlig
31
$nwat
10
$prmtop
ferr-l01.prm
$ligfil
lig.atoms
$crds
1
r1_cent.mdcrd 1 40
$prefix
l01
$explicit
1
$reffil
ref.pdb
$reflig
2455 2476
$siterad
4