Hi Leena,
If you are used to the linux terminal, you can do it this with a bash
script like this (file named *script.sh*):
*#!/bin/bash*
*ff="leaprc.gaff" #change your ff source line*
*resname="mol" #change your unit name line*
*#loop to generate leap.in <
http://leap.in> and execute*
*for pdbname in a*.pdb ; do*
*prefix=${pdbname%".pdb"} # pdb prefix, to generate respective prmtop and
crd*
*#add/remove options of your leap.in <
http://leap.in> if you need*
*cat > leap.in <
http://leap.in> << EOF*
*source ${ff}*
*${resname} = loadpdb ${pdbname}*
*loadamberparams ${prefix}.frcmod*
*saveamberparm ${resname} ${pdbname}.prmtop ${pdbname}.crd*
*quit*
*EOF*
*cat leap.in <
http://leap.in> #you can coment this line if dont wanna see
the inputs before they are runned*
*tleap -f leap.in <
http://leap.in>*
*done*
Save this file, give execution permissions (type: chmod +x script.sh),
and, in the same directory of your pdb files, run it (./script.sh)
I put some comments (text before #), sou you can manipulate it as you wish.
If you experience some trouble, contact me...
Regards!
Em sex, 23 de nov de 2018 às 08:55, Leena Aggarwal <leena.hrc.gmail.com>
escreveu:
> Dear Amber Users
> I have a list of pdb files whose name differs just by number like a1.pdb,
> a2.pdb, a3.pdb and so on. I have to generate topology files for each of
> them using same force field. Is there a way to generate these topology
> files by running a single script in tleap in one go??
>
> From
> Leena Aggarwal
> University of Delhi
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alechania Misturini
Mestranda em Físico-Química
Bacharel e Licenciada em Química
Grupo de Estrutura Eletrônica Molecular –〈
GE
⎜
EM
〉
*Departamento de Química – CFM*
*Universidade Federal de Santa Catarina – Brasil*
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Received on Fri Nov 23 2018 - 04:00:02 PST
