[gmx-users] Fatal error in grompp

[Justin Lemkul]

On 11/27/17 3:12 PM, Saumyak Mukherjee wrote:
> Dear Justin,
>
> Thanks for the reply.
>
> In that case, if I want the SOL-Backbone interaction energy, how shall I
> choose the energygrps? Is it possible to have such a group in the index.ndx
> file?

You have to have fully intact charge groups, which means including H 
atoms and whatever else the force field characterizes as a full charge 
group. You might be able to define such a group, but the quantity that 
comes out of the calculation probably doesn't have any physical meaning.

-Justin

> Regards,
> Saumyak
>
>
>
> ‌
>
> On 27 November 2017 at 19:05, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 11/27/17 5:25 AM, Saumyak Mukherjee wrote:
>>
>>> Dear All,
>>>
>>> I want to calculate the interaction energy between water and protein
>>> backbone. However, in mdp file, when I am using
>>>
>>> energygrps = SOL backbone
>>>
>>> ​grompp is returning the following error.
>>>
>>> Fatal error:
>>> atoms 1 and 2 in charge group 1 of molecule type 'Protein_chain_A' are in
>>> different energy groups
>>>
>>> Can someone kindly point out my mistake?​
>>>
>> You can't make the backbone a separate energy group. Look at what atoms 1
>> and 2 are - likely it's the N-terminal N and one H atom, which have to be
>> in the same group to do a group-based, pairwise energy decomposition.
>> Whatever groups you establish have to contain full charge groups.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>> --
>> 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.
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================