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

Nicolas Sapay nsapay at ucalgary.ca
Fri May 11 21:09:08 CEST 2007


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

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 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

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!



[ 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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