[AMBER] sleap and ptraj output issue with terminal residues

From: Kevin Wiehe <kevin.wiehe.duke.edu>
Date: Sat, 9 Jul 2011 00:45:54 -0400

I'm having pdb output issues with ptraj after building a prmtop with
sleap if I use the N or C preface to designate terminal residues. For
example if I use this line to define a sequence in my sleap input

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.

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'm using Amber Tools 1.5 and Amber 11.



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Received on Fri Jul 08 2011 - 22:00:03 PDT
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