[gmx-users] Re: topology and coordinate file not matching after grompp

[Justin Lemkul]

On 7/31/13 11:59 AM, chinnu657 wrote:
> renumber.gro <http://gromacs.5086.x6.nabble.com/file/n5010247/renumber.gro>
> topol_1AKI.itp
> <http://gromacs.5086.x6.nabble.com/file/n5010247/topol_1AKI.itp>
> topol_2CDS.itp
> <http://gromacs.5086.x6.nabble.com/file/n5010247/topol_2CDS.itp>
>
> I get the feeling you're not going to be able to see the files that I have
> uploaded here. If you prefer, I can send it to your personal email :)
>
> Thank you for your help and the time your putting.. I have attached allt eh
> files you asked for.
>

You've chopped off part of your protein:

   257ARG    NH2 3896   8.875   0.492  -2.033  0.0000  0.0000  0.0000
   257ARG   HH21 3897   8.820   0.535  -1.961  0.0000  0.0000  0.0000
   257ARG   HH22 3898   8.854   0.511  -2.129  0.0000  0.0000  0.0000
   257ARG      C 3899   8.936   0.127  -1.437  0.0000  0.0000  0.0000
   257ARG      O 3900   8.881   0.230  -1.398  0.0000  0.0000  0.0000
    8.63000   4.23400   4.31000

There are 129 residues and 1960 atoms in both proteins, thus you should have 
3920 atoms total.  You have lost the last Leu residue from the second protein, 
which accounts for your missing atoms.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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