AMBER Archive (2004)

Subject: Re: AMBER: using ptraj

From: Scott (spendley_at_uofu.net)
Date: Thu Jul 29 2004 - 16:15:17 CDT

Carsten,

   No problem here. You are trying to match up a coordinate file that
you just made that lacks water and ions with a paramter file that still
contains water and ions. Of course there will be a mismatch with the
number of ions.

Scott

On Tue, 2004-07-27 at 15:10, Carsten Detering wrote:
> Dear ambers,
>
> I have some trouble with a set of my trajectory files (complex, receptor
> and ligand), which I would like to prepare for mm_pbsa.
> this is my command sequence:
>
> ptraj my_parmfile_with_water_and_ions.prm
> trajin my_trajectory_file_from_sander.mdcrd
> trajout test.crd
> center :first_residue_in_complex-last_residue_in_complex
> image
> strip :WAT
> strip :Na+
> go
>
> When I then run mm-pbsa.pl, the calculation crashes, and the
> sander.1.out file contains the error message:
>
> FATAL: NATOM mismatch in coord and topology files
>
> I checked the output from ptraj concerning the number of atoms (when the
> program masks the atoms for imaging), and the NATOMS is the same as in
> the parameter files which dont contain waters and counter ions.
> Looking at the frames in vmd, it seems like all the water molecules (or
> at least a part of them) are concentrated in the protein now, and their
> atoms overlaying with the atoms of the protein.
>
>
> Could someone please point out to me what is wrong here?
>
> Thanks in advance,
>
> Carsten
>
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