[gmx-users] specbond .dat connection

[Mark Abraham]

Hi,

I would also strongly recommend replicating some existing work on heme with
Fe2+, before grappling with unknowns.

Mark

On Wed, Feb 8, 2017 at 3:25 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/8/17 1:47 AM, Mehreen Jan wrote:
> > Hello, anyone plz help Hopefully you all are doing well. I am using FF:
> 43a1
> > Spc watermodel version 5.0.7.
> >
> > I know parameters for Heme are already available and that is for FE2+. I
> want
> > to perform MD simulation for FE3+. While running simulation I get error :
> > Residue "OXY" not found in residue topology database. I checked .rtp
> file and
> > that does not include topology for OXY. I checked gromacs mailing list
> and
> > got the answer that modify specbond . dat file . Kindly please brief me
> how
>
> You have two separate problems.  A missing residue is not going to be
> fixed by
> altering specbond.dat.  You need to parametrize the residue appropriately
> and
> then add it to the .rtp file.  See
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> > should I modify specbond .dat file so that I could include oxygen
> molecule.
> > i read manual  5.6.7 Special bonds but i am still not able to connect OXY
> > with HEME.  This is my oxygen
> >
> > HETATM 2414  O1  OXY C1543       5.525  80.353  -6.212  1.00 25.38
> > O HETATM 2415  O2  OXY C1543       4.301  80.342  -6.721  1.00 30.35
> > O
> >
> > specbond .dat fie : any one plz modify it......
> >
>
> What have you tried based on the advice I gave you previously?  Anything
> specific that has failed?  Is there something unclear in the manual that
> can be
> improved?  If you want free help, you have to be willing to make some
> efforts on
> your own; no one's going to do your work for you.  We have multiple people
> posting identical questions (sometimes minutes apart, and people spamming
> my
> personal inbox incessantly) all asking for the same thing to be done, yet
> no
> progress seems to be made...
>
> -Justin
>
> > 9 CYS SG      1       CYS     SG      1       0.2     CYS2    CYS2 CYS
>       SG      1       HEM     FE      2       0.25    CYS2    HEME CYS
>   SG      1
> > HEM   CAB     1       0.18    CYS2    HEME CYS        SG      1
>  HEM     CAC     1       0.18    CYS2    HEME HIS        NE2     1       HEM
> > FE    1       0.2     HIS1    HEME MET        SD      1       HEM
>  FE      1       0.24    MET     HEME CO      C       1
> > HEME    FE      1       0.19    CO      HEME CYM     SG      1       CYM
> > SG      1       0.2     CYS2    CYS2 CYZ     SG      1       ZN1     ZN
> > 1       0.23    CYZ     ZN1
> >
> > Thanks, Mehreen Jan
> >
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>