Sorry, let' me correct something, I write the strings for prmtop and crd
files incorrectly...
Use this one:
*#!/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} ${prefix}.prmtop ${prefix}.crd*
*quit*
*EOF*
*cat leap.in <
http://leap.in/> #you can coment this line if dont wanna see
the inputs before they are runned*
*tleap -f leap.in <
http://leap.in/>*
*done*
Em sex, 23 de nov de 2018 às 09:33, Alechania Misturini <
alechaniam.gmail.com> escreveu:
> Hi Leena,
> If you are used to the linux terminal, you can do it this with a bash
> script like this (file named *script.sh*):
>
> *#!/bin/bash*
>
> *ff="leaprc.gaff" #change your ff source line*
> *resname="mol" #change your unit name line*
>
> *#loop to generate leap.in <http://leap.in> and execute*
> *for pdbname in a*.pdb ; do*
> *prefix=${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
>> _______________________________________________
>> AMBER mailing list
>> 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*
>
--
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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http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 23 2018 - 04:00:02 PST
