[gmx-users] Gro file does not match topology file... continue
jalemkul at vt.edu
Sat Jan 28 02:45:07 CET 2017
On 1/27/17 8:39 PM, Tasneem Kausar wrote:
> Yes , you are right. I was also surprised that when atoms in gro and
> topology match then how this error can be.
> In my case I was simulating a small peptide segment in water. Everything
> goes smoothly in it. Then I have generated a system with 8 peptides using
> genconf command.
> I have generated a box with editconf with -d 1.1 in a cubical box. In last
> line of topology file protein_chain_A was changed from 1 to 8. The genbox
> was used to solvate the system. Then grompp gives the mismatch error.
> Then with a box size of 2.1grompp was executed without any error.
> Same mdp file was used in both the case.
> This is the whole procedure, I have followed.
> This is why I was saying to increase the box size.
Without exact commands and error messages, there's no way to know what happened
except that whatever mistake you made the first time, you didn't make the
second. "Increase the box size" is not a solution for a mismatch between
coordinates and topology. Correct bookkeeping is.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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