[gmx-users] adding metal-bonding parameters to a force field
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Apr 3 19:25:01 CEST 2014
Hey Ahmet,
If you want to use virtual sites, you need to add a definition of a virtual
site for HZ1.
Cheers,
Tsjerk
On Apr 3, 2014 6:38 PM, "Ahmet yıldırım" <ahmedo047 at gmail.com> wrote:
> Dear users,
>
> I renamed a water molecule' atoms bound to the Zn +2 ion in starting pdb. I
> get the following error by pdb2gmx (with -vsite hydrogens). How can I fix
> it?
> ..
> Making bonds...
> Number of bonds was 2, now 2
> Warning: cannot convert atom 3 HZ1 (bound to a heavy atom OZ with
> 2 bonds and 2 bound hydrogens atoms) to virtual site
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.5
>
>
>
>
> HOH:OWZ
> O:OZ
>
> XXX.pdb:
> ..
> HETATM 2068 OZ OWZ A1001 -2.313 -0.628 16.011 1.00
> 8.54 O
> ...
>
> I modified as the following the some files.
>
> residuetypes.dat:
> OWZ water ;modified
>
> aminoacids.hdb:
> OWZ 1 ;modified
> 2 7 HZ OZ
>
> specbond.dat:
> ZN ZN 1 OWZ OZ 1 0.23 ZNOH2 ZOH2
> ;modified
>
> aminoacids.rtp:
> [ OWZ ];modified
> [ atoms ]
> OZ OZ -0.8824 0
> HZ1 HZ 0.5001 0
> HZ2 HZ 0.5001 0
> [ bonds ]
> OZ HZ1
> OZ HZ2
>
> atomtypes.atp:
> OZ 16.00000 ; modified
> HZ 1.00800 ; modified
>
> ffnonbonded.itp:
> OZ 8 16.00 0.0000 A 3.15061e-01 6.36386e-01
> ;modified
> HZ 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
> ;modified
>
>
>
> 2014-04-02 16:35 GMT+03:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 4/2/14, 9:25 AM, Ahmet yıldırım wrote:
> >
> >> Dear Justin,
> >>
> >> I did as you said but I get the following error when I run grompp
> command.
> >> I don't know where is my mistake. What should I do to solve it?
> >>
> >> Fatal error:
> >> Too many warnings (1), grompp terminated.
> >> If you are sure all warnings are harmless, use the -maxwarn option.
> >>
> >> Please see tables from the link:
> >>
> >>
> > It's pointless for anyone to try to troubleshoot any of this without the
> > actual error produced by grompp.
> >
> > -Justin
> >
> >
> > http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=
> >> web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F%
> >> 2Fpubmedcentralcanada.ca%2Fpicrender.cgi%3Fartinstid%
> >> 3D1482211%26blobname%3DNIHMS61946-supplement-File002.pdf&ei=
> >> DGs6U560PMHxhQejyIDABg&usg=AFQjCNGUfMCQZYegoRpLGg5D9GjpFsPCxQ&sig2=vr6-
> >> 1syRClNsDmFdMlWyXw&bvm=bv.63934634,d.ZG4
> >>
> >>
> >> OH: the Zn-bound hydroxide oxygen atom when Zn-bound water is
> >> deprotonated,
> >> OW: Zn-bound water oxygen,
> >> NA and NB: the nitrogen atoms directly bound to the Zn +2 ion (NE2 (NB)
> >> atoms
> >> in His94 and His96, ND1 (NA) atom in His119).
> >>
> >>
> >> Table 1: specbond.dat:
> >> 14
> >> HIS NA 1 ZN ZN 1 0.205 HISD ZNOH
> >> ;modified
> >> HIS NB 1 ZN ZN 1 0.205 HISE ZNOH
> >> ;modified
> >> ZN ZN 1 OH OH 1 0.18 ZNOH OH
> >> ;modified
> >> HIS NA 1 ZN ZN 1 0.205 HISD ZNOH2
> >> ;modified
> >> HIS NB 1 ZN ZN 1 0.205 HISE ZNOH2
> >> ;modified
> >> ZN ZN 1 OW OW 1 0.23 ZNOH2 HOH
> >> ;modified
> >>
> >>
> >> residuetypes.dat:
> >> ZNOH2 Ion ;modified
> >> ZNOH Ion ;modified
> >>
> >>
> >> Table 2: aminoacids.rtp:
> >> [ ZNOH];modified
> >> [ atoms ]
> >> ZN Zn 0.90920 1
> >> [ ZNOH2 ];modified
> >> [ atoms ]
> >> ZN Zn 0.89230 1
> >>
> >>
> >> Table 1: ffnonbonded.itp:
> >> OW 8 16.00 0.0000 A 1.76820e-01 6.371092e-01
> >> ;modified
> >> Zn 30 65.4 0.0000 A 1.10000e-01 5.23250e-02
> >> ;modified
> >>
> >> Table 1: ffbonded.itp:
> >> [ bondtypes ]
> >> ZN NA 1 0.20500 16744.00 ;modified
> >> ZN NB 1 0.20500 16744.00 ;modified
> >> ZN OH 1 0.18000 39348.40 ;modified
> >> ZN OW 1 0.23000 16744.00 ;modified
> >>
> >> [ angletypes ]
> >> C NA ZN 1 126.0 83.720 ;modified
> >> C NB ZN 1 126.0 83.720 ;modified
> >> NA ZN NB 1 109.5 96.278 ;modified
> >> NB ZN NB 1 109.5 96.278 ;modified
> >> NA ZN OH 1 109.5 96.278 ;modified
> >> NB ZN OH 1 109.5 96.278 ;modified
> >> ZN OH HW 1 124.0 83.720 ;modified
> >> HW OW HW 1 104.5 4186.0 ;modified
> >>
> >> [ dihedraltypes ]
> >> X ZN NA X 9 0.000 0.00000 3 ;modified
> >> X ZN NB X 9 0.000 0.00000 3 ;modified
> >> X ZN OH X 9 0.000 0.00000 3 ;modified
> >> X ZN OW X 9 0.000 0.00000 3 ;modified
> >>
> >>
> >>
> >> 2014-04-01 16:05 GMT+03:00 Justin Lemkul <jalemkul at vt.edu>:
> >>
> >>
> >>>
> >>> On 4/1/14, 8:49 AM, Ahmet yıldırım wrote:
> >>>
> >>> There are both Zn-OH(zinc-hydroxyl) and Zn-H2O (zinc-water) bond in
> >>>> structure, then should I modify "aminoacids.hdb" and "aminoacids.rtp"
> to
> >>>> add OH (hydroxyl) and water parameters?
> >>>>
> >>>>
> >>>>
> >>>> The parameters listed in Table 1 need to be added to ffbonded.itp and
> >>> ffnonbonded.itp. The thing to watch out for is that there are two
> >>> different H-O-H angles that are defined, depending on whether the water
> >>> is
> >>> free or bound to Zn. Therefore, you need unique atomtypes to
> >>> differentiate
> >>> between different types of water, so that requires modification of
> >>> atomtypes.atp, as well, if you will be processing the structure with
> >>> pdb2gmx.
> >>>
> >>> Table 2 corresponds to a specific residue that needs to be added as an
> >>> .rtp entry (again, only if you are using pdb2gmx to create the
> topology).
> >>> The .hdb entry is only necessary if you do not have H positions in
> the
> >>> input coordinate file.
> >>>
> >>> -Justin
> >>>
> >>>
> >>> 2014-04-01 11:03 GMT+03:00 Ahmet yıldırım <ahmedo047 at gmail.com>:
> >>>
> >>>>
> >>>> Firstly, I will change ffnonbonded.itp and ffbonded.itp. Later?
> >>>>
> >>>>>
> >>>>>
> >>>>> 2014-04-01 10:37 GMT+03:00 Ahmet yıldırım <ahmedo047 at gmail.com>:
> >>>>>
> >>>>> Dear users,
> >>>>>
> >>>>>
> >>>>>> Please see the file from the link:
> >>>>>>
> >>>>>> http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=
> >>>>>> web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F%
> >>>>>> 2Fpubmedcentralcanada.ca%2Fpicrender.cgi%3Fartinstid%
> >>>>>> 3D1482211%26blobname%3DNIHMS61946-supplement-File002.pdf&ei=
> >>>>>> DGs6U560PMHxhQejyIDABg&usg=AFQjCNGUfMCQZYegoRpLGg5D9GjpFs
> >>>>>> PCxQ&sig2=vr6-
> >>>>>> 1syRClNsDmFdMlWyXw&bvm=bv.63934634,d.ZG4
> >>>>>>
> >>>>>> I want to add table 1 and table 2 parameters to amber force field.
> How
> >>>>>> can
> >>>>>> I achieve it?
> >>>>>>
> >>>>>> --
> >>>>>> Ahmet Yıldırım
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>> --
> >>>>> Ahmet Yıldırım
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>> ==================================================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>
> >>> Department of Pharmaceutical Sciences
> >>> School of Pharmacy
> >>> Health Sciences Facility II, Room 601
> >>> 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!
> >>>
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> >>>
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> >>> send a mail to gmx-users-request at gromacs.org.
> >>>
> >>>
> >>
> >>
> >>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > 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/
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>
>
>
> --
> Ahmet Yıldırım
> --
> Gromacs Users mailing list
>
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