Re: [AMBER] Converting coordinate file generated into pdb format for nuparm

From: David A Case <>
Date: Thu, 17 Nov 2016 08:45:46 -0500

On Thu, Nov 17, 2016, ABHIJEET CHOWDHURY wrote:
> I want to convert my coordinate file generated into pdb format for
> nuparm but unable to find the right tool. I tried using ptraj but was
> unsuccessful. Although it created a pdb format but nuparm dose not
> accepts it as .pdb.

Use cpptraj or ambpdb from AmberTools16: these adhere more closely to
the standard PDB format than does the (very old) ptraj program. Use the
-bres flag to have residue names in the output PDB file match those in PDB

[Note: this may not work, since it looks(?) like you created the Amber files
with an old version of the program that still used residue names like "RA" for
adenosine (rather than the correct "A"). If ambpdb with the -bres flag
doesn't make the name "A", you will have to edit the files to make that change


AMBER mailing list
Received on Thu Nov 17 2016 - 06:00:05 PST
Custom Search