[gmx-users] adding SR2++ to charm27 force field

[Mark Abraham]

I asked to see the output. You can't be helped without someone seeing that.

Mark
On 15/04/2015 3:12 pm, "Ming Tang" <m21.tang at qut.edu.au> wrote:

> Hi Mark，
>
> pdb2gmx doesn't work， and it reminds the same error. Topol file was simply
> modified by mean from the topol file generated when considering MG2++
>
> Thanks
>
> Sent from my Huawei Mobile
>
> Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> Thanks. What is the whole pdb2gmx terminal output?
>
> Mark
>
> On Wed, Apr 15, 2015 at 3:05 AM, Ming Tang <m21.tang at qut.edu.au> wrote:
>
> > Dear Justin and mark,
> >
> > I modified the files like this:
> >
> > aminoacids.rtp
> >
> > [ MG ]
> >  [ atoms ]
> >         MG      MG      2.00    0
> > [ SR ]
> >  [ atoms ]
> >         SR      SR      2.00    0
> >
> > ions.itp
> >
> > [ moleculetype ]
> > ; molname   nrexcl
> > MG          1
> >
> > [ atoms ]
> > ; id    at type     res nr  residu name at name  cg nr  charge
> > 1       MG          1       MG          MG       1      2
> >
> > [ moleculetype ]
> > ; molname   nrexcl
> > SR          1
> >
> > [ atoms ]
> > ; id    at type     res nr  residu name at name  cg nr  charge
> > 1       SR         1       SR          SR       1      2
> >
> > ffnonbonded.itp
> >
> > CP1     MG      1       0.274842254546  0.051243325419
> > CP1     SR      1       0.310269        0.494658
> > whenever there is MG, I add SR.
> >
> > ffnanonbonded.itp
> >
> > CN7     MG      1       0.274842254546  0.051243325419
> > CN7     SR      1       0.310269        0.494658
> > whenever there is MG, I add SR.
> >
> > atomtypes.atp
> >
> > MG      24.305000 ;     Magnesium Ion
> > SR          87.62000  ;           Strontium Ion
> >
> > When I copy the modified force field to the working directory,  the PDB
> > file used to consider MG Cannot be minimised too, which works well with
> the
> > original Charmm27 force field. It reminds that atomtype SR not found
> again.
> > I use ready-made pdb file and topol file for minimization.
> >
> > thanks
> >
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin
> > Lemkul
> > Sent: Wednesday, 15 April 2015 1:22 AM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] adding SR2++ to charm27 force field
> >
> >
> >
> > On 4/14/15 5:12 AM, Ming Tang wrote:
> > > Hi Mark,
> > >
> > > Thanks for your reply. I am sure as I changed the files in the
> > charmm27.ff installed in my unbuntu system. Is there any other things I
> > need to consider?
> > >
> >
> > The files you listed are the only ones that should need to be modified.
> > Either you missed a step and think you did something you didn't, or your
> > changes didn't actually take effect (modifying the top-level installation
> > usually requires admin privileges, so if you tried to modify without sudo
> > or root it won't take).
> >   Experiment with a local copy of the directory rather than potentially
> > messing up something system-wide.  The error points most likely to the
> .atp
> > file.
> >
> > -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 | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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