AMBER Archive (2004)

Subject: Re: AMBER: using ptraj

From: Carsten Detering (detering_at_u.washington.edu)
Date: Thu Jul 29 2004 - 17:11:11 CDT

Scott,

thanks for the reply.
Actually, this was not the case. I tried on the one hand to calculate
the three files *without* the waters and ions (i.e. the naked
molecules/complex), and on the other hand *with* waters and ions. I used
the respective parameter files in both cases and got the error in both
cases.

Carsten

Scott wrote:

> 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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>
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