On 20/12/2010 4:25 PM, vinothkumar mohanakrishnan wrote:
Hi all
I want to use pdb2gmx to generate hexane topology and hexane.gro file.
i have added the atom name in .atp file and corresponding section in
.rtp file. i have given below my .rtp entry
You don't need to add an .rtp entry, it's as much work as writing your
molecule's .itp file and more fiddly.
[ DRG ]
[ atoms ]
CAA opls_966 0 1
CAF opls_966 0 1
CAB opls_967 0 2
CAC opls_967 0 2
CAD opls_967 0 2
CAE opls_967 0 2
[ bonds ]
CAA CAB
CAB CAC
CAC CAD
CAD CAE
CAE CAF
[ angles ]
CAA CAB CAC
CAB CAC CAD
CAC CAD CAE
CAD CAE CAF
[ dihedrals ]
CAA CAB CAC CAD
CAB CAC CAD CAE
CAC CAD CAE CAF
but i get the error message as given below and it doesn't generate any
.top and .gro file . I searched the mailing list and found a similar
post but there is no solution
(http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html)
previously i used pdb2gmx for other molecules and it worked fine for
the oplsaa force field. any help is highly appreciated.
Opening library file ffoplsaa.rtp
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading hexane.pdb...
Read 6 atoms
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 6 atoms
chain #res #atoms
1 ' ' 1 6
All occupancies are one
Opening library file ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.7
Source code file: resall.c, line: 279
Fatal error:
in .rtp file at line:
-------------------------------------------------------
Probably you've mangled the file somehow, like editing on a non-unix
system and not changing the line endings, or transferred zero bytes of
the file.
PRODRG will be worthless for generating parameters for any force field
other than that which it targets. See
http://www.gromacs.org/Documentation/How-tos/Parameterization for
general advice. I'd suggest throwing away what you've been trying to do,
and seeking a force field that already has hexane-suitable parameters,
preferably with someone else having already published using those
parameters. If your literature search comes up empty, perhaps you should
choose your force field according to the availability of useful
parameterization tools (see
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation),
rather than inventing some Frankenstein approach that your reviewer is
likely to just laugh at.
Mark
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
