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

Nicolas Sapay nsapay at ucalgary.ca
Tue May 15 00:50:20 CEST 2007

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!



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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