[gmx-users] produce charrmm topology
Justin Lemkul
jalemkul at vt.edu
Thu Aug 11 13:46:06 CEST 2016
On 8/11/16 4:37 AM, a.omidi at shirazu.ac.ir wrote:
> Thankyou
> I have some problem about pythoon and packages of that for converting it, if I
> couldnt do that, I will ask you.
> now I have an other problem:
> I have defined a new residue included of an ASN + 5 sugures, I have used
> charmm36 ff , but I need to add bonds, angles and dihedrals of that new residue
> to the ffbonded.itp.
> I have asked you How I can do this,and you said me to read the manual.
> I couldnt undrestand.
> But now, I undrestood this "( 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>)"
> may dothat, but the types of atmos that cgenff recognizes is differnt of that of
> charmm36 ff.
> I wonder if I can use cgenff for taking bonds, angles and dihedrars for my new
> residue? and becuase of being differnt between the types of atoms, How can I
> solve this problem?
>
You should not be using CGenFF for a glycosylated protein residue. The CHARMM
force field already supports that fully (and the larger point is you should not
mix CGenFF with CHARMM for the purposes of creating a constituent residue;
CGenFF is only for ligands, co-solvents, etc.)
Try building your system with the CHARMM-GUI server instead. It will be much
easier than trying to create the necessary .rtp entry for a complex
carbohydrate. This is one area in which CHARMM is vastly superior to GROMACS.
-Justin
> On Mon, 08/08/2016 03:02 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> On 8/8/16 2:11 AM, a.omidi at shirazu.ac.ir <mailto:a.omidi at shirazu.ac.ir> wrote:
> > Hi
> > thanks alot , I could do it,with this server ( 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>
> > and its format is .str
> > now I need .itp of my ligand for runing it,
> > I dont know if it is possible to use .str instead of .itp ??
> > could you please tell me what I should do?
> >
>
> Convert it.
>
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>
> -Justin
>
> > On Sun, 08/07/2016 04:19 AM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> >
> > On 8/7/16 2:50 AM, a.omidi at shirazu.ac.ir <mailto:a.omidi at shirazu.ac.ir>
> <a.omidi at shirazu.ac.ir> <mailto: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 <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> > <jalemkul at vt.edu> <mailto:jalemkul at vt.edu>>> wrote:
> > >
> > > On 8/2/16 2:35 AM, a.omidi at shirazu.ac.ir <mailto:a.omidi at shirazu.ac.ir>
> <a.omidi at shirazu.ac.ir> <mailto:a.omidi at shirazu.ac.ir>>
> > <a.omidi at shirazu.ac.ir> <mailto:<a.omidi at shirazu.ac.ir>>
> <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>
> > <jalemkul at outerbanks.umaryland.edu>
> <mailto:jalemkul at outerbanks.umaryland.edu>>
> > <jalemkul at outerbanks.umaryland.edu>
> <mailto:<jalemkul at outerbanks.umaryland.edu>>
> <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
> <mailto:jalemkul at outerbanks.umaryland.edu>
> <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 <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
==================================================
More information about the gromacs.org_gmx-users
mailing list