[gmx-users] Re Grompp errors while changing combination rules

[Justin Lemkul]

On 7/18/18 2:18 AM, Apramita Chand wrote:
> Dear Justin,
> I have tried the same commands with gromacs version 5.1.2 and the same
> errors arise.
> You have suggested that the format of what has been provided to grompp may
> be wrong. What I did was modify ffnonbonded.itp by leaving the C6, C12
> columns empty alongside pair interactions under the [nonbonded params] and
> [pairs] headings. (Since I have specified sigma,epsilon values in the
> [atomtypes] section(intending to use combination rule 3), the interaction
> parameters have to be calculated using these values.)  For example:
>
>
>
>
>
>
>
>
>
> *[ nonbond_params ]; i    j func          c6           c12      OM
> O  1      OA        O  1      OA       OM  1      OE        O  1
> OE       OM  1      OE       OA  1*

This isn't syntactically correct. You need to specify the actual 
parameters. The [nonbond_params] section is intended to *replace* 
combination rule values. You can't leave it blank.

>
> *.... etc. *
>
>
>
>
>
>
>
>
>
>
> *and [ pairtypes ]; i    j func             OM        O      OA        O
> 1      OA       OM  1      OE        O  1      OE       OM  1      OE
> OA  1      OW        O  1*

As above, you need to supply the parameters.

-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.thelemkullab.com

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