Thanks Alechania. The script is really helpful and it solved my problem.
On Fri, Nov 23, 2018 at 5:10 PM Alechania Misturini <alechaniam.gmail.com>
wrote:
> 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*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 23 2018 - 22:00:02 PST
