[gmx-users] produce charrmm topology

[Justin Lemkul]

On 8/7/16 2:50 AM, a.omidi at shirazu.ac.ir wrote:
> Hi
> Icouldnt did that with" https://cgenff.paramchem.org/
> <https://webmail.shirazu.ac.ir/redir.hsp?url=%68%74%74%70%73%3A%2F%2F%63%67%65%6E%66%66%2E%70%61%72%61%6D%63%68%65%6D%2E%6F%72%67%2F>"
> I had this error:
> "Error / Warning 3QRH_C.err
> <https://cgenff.paramchem.org/initguess/#20160807/3QRH_C.err> Now processing
> molecule /scrat ...attype warning: carbon radical, carbocation or carbanion not
> supported;skipped molecule. .."
> cold you tell me How I can produce topology of my ligand with this server.
>  I dont know what I should do...
>

You have some sort of bizarre molecule that the force field doesn't support. 
make sure the input .mol2 file specifies the correct connectivity.

-Justin

>
> On Tue, 08/02/2016 04:00 PM, Justin Lemkul &lt;jalemkul at vt.edu&gt; wrote:
>
>     On 8/2/16 2:35 AM, a.omidi at shirazu.ac.ir <mailto:a.omidi at shirazu.ac.ir> wrote:
>     > ​Hi
>     > I have produced a ligand by ATB
>     > now I want to run it with charmm36 ff
>     > cold you tell me How I can convert gromos topology to charmm topology?
>
>     You can't. GROMOS and CHARMM use a fundamentally different form (united-atom
>     vs. all-atom) and have very different parametrization strategies. If you want a
>     CHARMM topology, generate it using e.g. https://cgenff.paramchem.org/
>
>     -Justin
>
>     --
>     ==================================================
>
>     Justin A. Lemkul, Ph.D.
>     Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>     Department of Pharmaceutical Sciences
>     School of Pharmacy
>     Health Sciences Facility II, Room 629
>     University of Maryland, Baltimore
>     20 Penn St.
>     Baltimore, MD 21201
>
>     jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu>
>     | (410) 706-7441
>     http://mackerell.umaryland.edu/~jalemkul
>
>     ==================================================
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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