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

Justin Lemkul jalemkul at vt.edu
Wed Jul 31 17:34:05 CEST 2013

On 7/31/13 11:29 AM, chinnu657 wrote:
> Hi Justin,
> Oh, I see. I am going to paste my commands here.
>   pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce
>   pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce
>   editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0
>   editconf -f 2CDS_conf.gro -o conf1.gro -center 7.5 0 0
>   cat conf1.gro conf2.gro > system.gro
>   genconf -f system.gro -o renumber.gro -renumber
>   editconf -f renumber.gro -o newbox.gro -c -d 1.0 -bt dodecahedron
>   genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solvated.gro
>   grompp -f ions.mdp -c solvtaed.gro -p topol.top -o ions.tpr
> It is after this that I get the error

If you send me renumber.gro and both protein .itp files (off-list), I will have 
a look and try to figure out where the problem lies.  In theory, the above 
commands should work, provided that the modifications following concatenation 
were correct, though if genconf didn't complain, whatever you did is probably 
fine, at least from a syntactical standpoint if not a topological one.



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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