[gmx-users] (no subject)

[Navneet Kumar Singh]

Thank You Sir!

Attached file can be downloaded from following link.

https://fil.email/OR7Nsh0f
<https://fil.email/OR7Nsh0f?&showconfirmation=true>
____________________________________________________________________
Error

ERROR 1 [file unk.itp, line 497]:
  Duplicate atom index (23) in virtual_sites3
___________________________________________________________________

It support lone pair construction for halogens only. Please suggest some
alternatives.

On Sun, Aug 25, 2019 at 8:11 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/25/19 8:33 AM, Navneet Kumar Singh wrote:
> > can you please help in solving this error while running MD simulation of
> > protein-ligand complex using CHARMM36 force field on GROMACS engine.
> >
> >
> >
> > *Command*
> >
> > *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr*
> >
> >
> > *ERROR*
> >
> >
> > *ERROR 1 [file unk.itp, line 497]:  Duplicate atom index (23) in
> > virtual_sites3*
> >
> >
> >
> *------------------------------------------------------------------------------------*
> >
> > *unk.itp file indicated error/ Please find the attached file for more
> > details.*
>
> The mailing list does not accept attachments.
>
> Please see the information at
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs which
> specifically addresses this lone pair issue and how to deal with it.
> GROMACS does not easily support the kinds of lone pair/vsite
> construction that CHARMM requires for this kind of interaction.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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-- 






     Thanks & Regards
_______________________________________________________

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneetcdl at gmail.com  <navneetcdl at gmail.com>
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

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