Hi, Nguyen
Thank you, it works for the distance calculations though I got some
warnings. These distance measurements were quite same as that obtained from
CHIMERA or VMD.
Thank you,
Mahendra Thapa
University of Cincinnati, OH
On Wed, Mar 18, 2015 at 12:38 PM, Thapa, Mahendra (thapamb) <
thapamb.mail.uc.edu> wrote:
>
>
>
> ________________________________________
> From: Hai Nguyen
> Sent: Wednesday, March 18, 2015 10:37:58 AM (UTC-06:00) Central America
> To: AMBER Mailing List
> Subject: Re: [AMBER] how to use cpptraj for pdb files generated from
> external software
>
> Hi
>
> I believe you can you the pdb file as Topology file too. Something like
>
> parm your_pdb_file.pdb
> trajin your_pdb_file.pdb
>
> Hai
>
> On Wed, Mar 18, 2015 at 12:34 PM, Mahendra B Thapa <thapamb.mail.uc.edu>
> wrote:
>
> > Dear Amber users,
> >
> > I have some hundreds of pdb files generated from external software (like
> > online server), these pdb files differ from pdb generated by AMBER in
> term
> > of naming of hydrogen atom. Is there a way to generate topology file for
> > these files so that I could use ambertool like cppraj command to
> calculate
> > atomic distances, angles etc to compare with corresponding AMBER
> results ?
> > For a single pdb, I use leap to get topology file but do not know for a
> > large no of pdb files.
> >
> > Thank you for help,
> > Mahendra Thapa
> > University of Cincinnati
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Mar 18 2015 - 10:00:05 PDT
