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

Nicolas Sapay nsapay at ucalgary.ca
Tue May 15 01:02:33 CEST 2007

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 


Sorry for the inconvenience


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

More information about the gromacs.org_gmx-users mailing list