Jennifer Williams wrote:
Hi,
I am trying to use the pdb2gmx to generate a .top file from my .pdb.
I am getting the following error?.
All occupancies are one
Opening library file /home/jwillia4/gromacs/share/gromacs/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file /home/jwillia4/gromacs/share/gromacs/top/ffoplsaa.rtp
Residue 56
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: resall.c, line: 138
Fatal error:
Atom type opls_23 (residue MCM) not found in atomtype database
As my residue is not already present I have added the following to the
end of the ffoplsaa.rtp file
[ MCM ]
[ atoms ]
OH opls_23 -0.70 1
HO opls_24 0.435 1
SI SI 0.832 1
OS opls_62 -0.400 1
[ bonds ]
SI OS
SI OH
OH HO
[ dihedrals ]
OS SI OH HO
SI OS SI OS
SI OS SI OH
OH SI OH HO
The following is already present in the ffoplsaabon.itp file (standard
version);
; This bit added by DvdS for quartz simulation 2005-05-07
; These parameters are taken from GROMOS and were also used in
; Wensink et al. Langmuir 16 (2000) pp. 7392-7400
;
[ bondtypes ]
; i j func b0 kb
SI OS 1 0.16300 251040. ; From GROMACS
SI OH 1 0.16300 251040. ;
[ angletypes ]
; i j k func th0 cth
SI OS SI 1 155.000 397.480
OS SI OS 1 109.500 397.480
OH SI OS 1 109.500 397.480
SI OH HO 1 109.500 397.480
[ dihedraltypes ]
; i j k l func coefficients
; Added DvdS for Quartz simulations
SI OS 1 0.000 3.766 3
SI OH 1 0.000 3.766 3
And the entries in the .atp file which I am getting the error message
about are already there (they are in the standard version-I didn?t need
to add them myself). So I can?t figure out why they are not being read.
I also tried adding the name of my residue (MCM) to aminoacids.dat and
incrementing the count at the top.
Do I need to make any other changes?
Thanks
It looks fine. In theory you might want to edit the hdb file as wel if
you want to automatically add H, but I presume you have them already in
which case it is not necessary.
Which gromacs version are you using?
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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