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
manually.
Nicolas
Sorry for the inconvenience
Nicolas
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
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