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

David van der Spoel spoel at xray.bmc.uu.se
Sun May 13 07:54:30 CEST 2007

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

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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