Re: [AMBER] sleap and ptraj output issue with terminal residues

From: case <>
Date: Sun, 10 Jul 2011 21:39:10 -0400

On Sat, Jul 09, 2011, Kevin Wiehe wrote:
> pep = sequence { NGLY THR CALA }
> After the simulation, if I output my trajectory as a series of pdb
> files using ptraj, I will get residue names of "NGLY" and "CALA"
> instead of the three letter standard pdb format "GLY" and "ALA" in the
> pdb files. I think the problem lies in how sleap outputs the
> RESIDUE_LABEL section of the prmtop file which seems to be different
> from how tleap does it.

Thanks for the report.
> I'd like to...
> 1) alert your attention to this formatting issue if it's not known already
> 2) confirm that this shouldn't have affected the actual simulation or
> energy calculations, only the output format of the labels afterwards.

I agree that the simulation should be fine.


AMBER mailing list
Received on Sun Jul 10 2011 - 19:00:04 PDT
Custom Search