Project

General

Profile

posre.sh

simple script to demonstrate issue in gmx genrestr - Joe Jordan, 11/05/2018 07:41 PM

 
1
#!/bin/bash
2

    
3
gmx='/tmp/current/bin/gmx'
4

    
5
pdb='chainTer.pdb'
6
itpA='topol_Protein_chain_A.itp'
7
itpB='topol_Protein_chain_B.itp'
8

    
9
$gmx pdb2gmx -f $pdb -ff 'amber03' -water 'tip3p'
10

    
11
#works
12
protein_ca_sel='chain A and name CA'
13
current='ca-A'
14
$gmx select   -s $pdb -on $current.ndx -select "$protein_ca_sel"
15
$gmx genrestr -f $pdb -n  $current.ndx -o posre_$current.itp
16
echo -e "; Include Position restraint file
17
#ifdef POSRES_CA
18
#include \"posre_$current.itp\"
19
#endif\n" >> $itpA
20
$gmx grompp -f ca.mdp -c conf.gro -p topol.top -o ca-A.tpr -r conf.gro
21

    
22

    
23
#fails
24
protein_ca_sel='chain B and name CA'
25
current='ca-B'
26
$gmx select   -s $pdb -on $current.ndx -select "$protein_ca_sel"
27
$gmx genrestr -f $pdb -n  $current.ndx -o posre_$current.itp
28
echo -e "; Include Position restraint file
29
#ifdef POSRES_CA
30
#include \"posre_$current.itp\"
31
#endif\n" >> $itpB
32
$gmx grompp -f ca.mdp -c conf.gro -p topol.top -o ca-B.tpr -r conf.gro
33