[gmx-users] topology of ligand contains boron

[André Farias de Moura]

It is not polite to ask again after just a few hours, since we are here
doing this for free (you cannot push people into answering your questions,
after all they are yours, not ours).

If you have chosen to work with an exotic molecule with missing parameters
of any kind, it is you job to fill the gaps in your topology file, there is
no such automatic tool doing that. You should start digging the literature,
either to find the missing parameters or to learn how to derive them.

On Mon, Nov 30, 2015 at 10:09 AM, subho_1997 at yahoo.com <subho_1997 at yahoo.com
> wrote:

> Hi all,
>
> Can someone please answer my question, about how to find forces on the
> atoms of the "frozen" molecule/group.
>
> Thanks
> Subn
>
>
>
> Sent from my HTC
>
> ----- Reply message -----
> From: "Low Chen Fei" <lowcf84 at ukm.edu.my>
> To: <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] topology of ligand contains boron
> Date: Mon, Nov 30, 2015 3:19 AM
>
> Dear,
> im currently running MD simulation of protein-ligand complex. but the
> ligand that im running contain boron. i failed to obtain the ligand
> topology from PRODRG, thus my analysis cant progress since then. would like
> to ask for opinion how can i solve this situation.?
>
> thanks.
>
> Best regards,
> Low Chen Fei, PhD
> Post-Doctoral Fellow
> Institute of Systems Biology (INBIOSIS)
> Universiti Kebangsaan Malaysia
> Bangi 43600
> Selangor Darul Ehsan
> Malaysia
> Mobile: 601128013969
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090