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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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