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

[Ming Tang]

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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