[AMBER] issues with MMPBSA and explicit waters

From: Alfredo Quevedo <alfredoq.fcq.unc.edu.ar>
Date: Mon, 02 Sep 2013 11:39:19 -0300

Dear Amber users, I am facing a problem with an MMPBSA calculation when
keeping explicit water molecules. The procedure I am following to
perform the decomposition analysis is:

1: center and image the explicit MD trajectory,
2: use cpptraj to identify "closest" water molecules, write stripped
.prmtop file and resulting trajectory,
3: generate "complex", "receptor" and "ligand" .prmtop files using
ante-MMPBSA.py (without stripping waters),
4: run the MMPBSA.py module, settinf the "strip_mask" keyword to non
default parameters so as to keep explicit waters.

When I performed the above mentioned procedure keeping just 1 explicit
water (closest 1: in step 2), the calculation finished without any
problem and calculated components seemed to be ok.
My problem originates when I want to keep 2 or more explicit water
molecules in the trajectory, in which when running step 4, the
calculation for the complex finishes ok, but when the calculation for
the receptor starts I get the error "bad atom type: HW". This error
originates from sander when trying to run the decomposition calculatioin
from the files created by MMPBSA.py (_MMPBSA_gb_decomp_rec.mdin,
_MMPBSA_dummyreceptor.inpcrd). I inspected the generated files with VMD
using receptor.prmtop and everything seems to be ok. I cant understand
why sander gets an "atom type" error if everything was ok for the
simmulation corresponding to the complex.
Has anyone faced this problem before?.

Thank you very much in advance for the help,

kind regards


AMBER mailing list
Received on Mon Sep 02 2013 - 08:00:02 PDT
Custom Search