[gmx-users] Gro file does not match topology file... continue
tasneemkausar12 at gmail.com
Sat Jan 28 04:22:13 CET 2017
You both are right. Previously I was editing the topology file after
solvating the protein.
So the mismatch error was there.
Sorry for the inconvenience...........
On Sat, Jan 28, 2017 at 7:14 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users