[gmx-users] Fwd: Fatal error: number of coordinates in coordinate file (trp-b4ion.pdb, 25093) does not match topology (trp.top, 26684)

[Justin Lemkul]

On 7/29/13 6:30 AM, Jonathan Saboury wrote:
> Files: http://www.sendspace.com/file/vxcnv3
>
> Commands used: http://pastebin.com/raw.php?i=wPqfuUwc
>
> What I want to do: I just want to run the protein without the ligand in
> explicit water. Why is the coordinate file not matching topology?
>
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topologydoesn't
> offer much help in this case. I know the problem is the number of
> waters however.
>

The problem is not the waters.  Your topology specifies 3221 protein+CA atoms, 
but the coordinate file you're using only has 1630.  The problem is here:

pdb2gmx -ff amber99sb -f protein2.pdb -o trp.pdb -p trp.top -water tip3p -ignh

editconf -bt octahedron -f protein2.pdb -o trp‐b4solv.pdb -d 1.0

You're using "protein2.pdb" to move forward, after pdb2gmx acted upon it (to 
produce conf.gro) to add hydrogens.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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