[gmx-users] carbon atom not found by pdb2gmx and modification of specbond.dat

Tue May 15 06:21:52 CEST 2007

Hi Nicolas,

Have a look at the ff*bon.itp of your choice and go all the way to the
bottom. You can see there how the connections are handled further for
e.g. heme and can add the angles and dihedrals you want.

Also, you report bonds between the zinc and a number of other atoms.
This is probably due to the viewer you use, which bases connectivity
on the distances between atoms. This has nothing to do with a
topology.

Cheers,

Tsjerk

On 5/15/07, Nicolas Sapay <nsapay at ucalgary.ca> wrote:
> Sorry, the message has been sent too fast, the 4 bonds have been
> correctly created now. So, the correct specbond line is:
> CYS     SG      1       ZN2     ZN      1       0.25     CYSZ    ZN
>
> There is still an angles that lacks (the S-ZN-S angle), but I can add it
> manually.
>
> Nicolas
>
> Sorry for the inconvenience
>
> Nicolas
>
> Nicolas Sapay wrote:
> > Thnaks for your answer,
> >
> > I have solved the problem with the lacking CD1 atom. There was a weid
> > end of line the line jus before. But pdb2gmx is still unable to link
> > correctly the ZN2 residue with the 4 CYS. The distance between SG and
> > ZN atoms are computed correctly (I have the bon lenght to 0.25 nm) and
> > SG-ZN bonds has been introduced in the topology file.  However,
> > pdb2gmx also introduces bonds between the ZN and CB, HB1, HB2 atoms of
> > the 4 Cys, though theses distances don't appear in the distance
> > matrix. I have modified specbond.dat as following :
> >
> >    CYS     SG      1       ZN2     ZN      1       0.2     CYSZ    ZN2
> >    (previsously : CYS     SG      1       ZN2     ZN      4
> > 0.2     CYSZ    ZN2)
> >
> > Supposing that "4" means "create 4 bond with", but nothing change. Any
> > suggestion are welcomed!
> >
> > Thanks
> >
> > Nicolas
> >
> > David van der Spoel wrote:
> >> Nicolas Sapay wrote:
> >>> Hello,
> >>>
> >>> I'm trying to create a topology file of a system made of a protein
> >>> homodimer (2x198 residues), water (TIP3P x 900) and some ions (CLA,
> >>> SOD, ZN2). The system has been initially built with CHARMM and all
> >>> hydrogens are already included. I use an implementation of CHARMM
> >>> for Gromacs (i.e. ffcharmm.rtp, .itp, .hdb, .tdb). My objective is
> >>> to check if it is easy to use pdb files previously built with CHARMM
> >>> with my implementation of the CHARMM ff in Gromacs. That is why I
> >>> use a difficult system with dimer, cys-cys bridges, zinc finger, etc...
> >>>
> >>> I use the following command  to create the topology file:
> >>>
> >>>    pdb2gmx -f ns5a.pdb -o ns5a.gro -p ns5a.top -water tip3p -ignh -ff
> >>>    charmm27
> >>>
> >>>
> >>> I have a first problem with the 2 zinc fingers. pdb2gmx find the 2
> >>> cys-cys bridges without trouble but failed with the bonds between
> >>> the ZN2s and the CYSs. I have modified specbond.dat as following:
> >>>
> >>>    CYS     SG      1       ZN2     ZN      4       0.2     CYSZ    ZN2
> >>>
> >>>
> >>> with ZN2, the residue name of the Zn ion and CYSZ, the residue name
> >>> for coordinated CYSs. Both residues are defined in ffcharmm27.rtp.
> >>> However, I haven't found documentation on how to modify
> >>> specbond.dat. So, I have guessed what the different parameters mean
> >>> and I'm pretty sure to have done something wrong. Can someone
> >>> correct my specbond definition and tell me what the different
> >>> parameters signify?
> >> the 0.2 is the bondlength and currently there is a hard toloerance of
> >> 10% on that. Check the special bond matrix to see what happens.
> >>
> >>>
> >>> The second problem comes when pdb2gmx try to add hydrogens. It
> >>> crashes with the following message :
> >>> WARNING: atom CD1 not found in residue 84 while adding atom
> >>> -------------------------------------------------------
> >>> Program pdb2gmx, VERSION 3.3.1
> >>> Source code file: genhydro.c, line: 304
> >>>
> >>> Fatal error:
> >>> Atom CD1 not found in residue TRP84 while adding hydrogens
> >>> -------------------------------------------------------
> >>
> >> is your ffcharm27.hdb file correct? since you already have hydrogens
> >> you probably don't need to add them.
> >>
> >>>
> >>> However, the CD1 atom is indeed present in the pdb file and TRP
> >>> residues upstream to TRP84 are perfectly treated. Additionally HD1
> >>> atoms is properly defined in the .hdb file. I have tried to create
> >>> the .top file on a single monomer and it works perfectly. I have
> >>> also tried to merge the homodimer using the -merge option of pdb2gmx
> >>> but it crashes again on the second TRP84... Any suggestion are
> >>> welcomed!
> >>>
> >>> Thanks
> >>>
> >>> Nicolas
> >>>
> >>
> >>
> >
> >
>
>
> --
> [ Nicolas SAPAY, Ph.D. ]
> University of Calgary, Dept. of Biological Sciences
> 2500 University drive NW, Calgary AB, T2N 1N4, Canada
> Tel: (403) 220-6869
> Fax: (403) 289-9311
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623