On Tue, 2014-03-11 at 12:45 +0330, Saeed Nasiri wrote:
> Dear Jason Swails
>
> Thanks for your quick replying. I did the commands and run minimization
> step successfully, but in the simulation the "Error: Bad topology file. Sum
> of ATOMS_PER_MOLECULE does not equal NATOM." was appeared. I don't know
> what should I do?
I think what is happening is that cpptraj detects that all atoms are
ordered continuously with respect to the molecules so cpptraj does not
complain. However, the ATOMS_PER_MOLECULE section is still corrupt so
sander and pmemd refuse to run. I believe cpptraj does not detect this
problem because it ignores the data in SOLVENT_POINTERS and
ATOMS_PER_MOLECULE and just determines molecularity on its own.
In this case, the only available option to fix your topology file is to
use ParmEd. Since your solvent is not water (let's assume that one of
your solvent residues is named ION) you need to define your solvent to
ParmEd first. So your parmed script should look something like below:
=== parmed.in ===
parm your.prmtop
defineSolvent :ION
setMolecules solute_ions True
parmout fixed.prmtop
=================
Then run ParmEd with the command
parmed.py -i parmed.in
The "fixed.prmtop" that it creates should be usable in sander and pmemd.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 11 2014 - 05:00:03 PDT
