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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Received on Wed Mar 18 2015 - 10:00:03 PDT
