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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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