AMBER Archive (2008)

Subject: Re: AMBER: problems with ptraj and strip waters

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Sep 18 2008 - 16:29:56 CDT

steve- not sure what's going wrong, but here are some thoughts:

use ambpdb to make a pdb file from your solvated prmtop/restart. delete the
waters, and see how many atoms are in the pdb. (use pdb since you can tell
where the water starts). then compare this to the number of atoms in your
nowater prmtop. you could also just load 1 frame in ptraj (not the whole
traj) by using the start/stop flags to trajin, and trajout to a pdb file,
not a trjaectory format. look at the pdb and see if it looks like what you
get from ambpdb on your nowater prmtop/crd that you created with leap. or,
you might get the info you need from the ATOMS_PER_MOLECULE flag in the 2
prmtop files. they should match for your solvated/not prmtops, except for
the 3s.

is there any more info in the VMD console when you try to load the
trajectory? I still can't imagine why it would want #atoms from a trajectory
file- it's not there.

do you have any ions (anything not called WAT) that might differ from the
solvated/not systems?

On Thu, Sep 18, 2008 at 5:19 PM, Steve Seibold <seibold_at_chemistry.msu.edu>wrote:

> Thanks for your comments, Carlos
>
>
>
> I tried on a Window VMD and a Linux VMD and in both cases when I added the
> topology file first with"Amber7 parm" followed by the "Amber Coordinates", I
> got the same error "....number of atoms could not be dtermined".
>
>
>
> This topology file (without water) recognizes the mdcrd when I use rdparm
> and reads out how many frames.
>
>
>
> Also, VMD has no problem reading the topology files and correct states
> residues etc.
>
>
>
> My input file is as follows for making the trajectories without water:
>
>
>
> *trajin file.mdcrd*
>
> *strip :WAT*
>
>
>
> *center :1-2495 mass origin*
>
> *image origin center familiar*
>
>
>
> *trajout file_no_water.mdcrd nobox*
>
>
>
> *go*
>
>
>
>
>
> Steve Seibold
>
> Research Asst. Professor
>
> seibold_at_chemistry.msu.edu
>
> 19B Chemistry Building
>
> Michigan State University
>
> East Lansing, MI 48824
>
> Office 517-355-9715 ext 264
>
>
>

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