[gmx-users] Gro file does not match topology file... continue

[Tasneem Kausar]

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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> School of Pharmacy
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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