vinothkumar mohanakrishnan wrote:
Hi Justin
I had taken United atom pdb file form PRODRG and i want to use OPLS-UA
Interesting choice. That's an antiquated force field...
force field. i dont know what's wrong out there.I have done it befor for
other molecules like DCE, CCL4 etc.
To create a topology for a simple six-atom molecule, pdb2gmx is unnecessary.
Just write the topology by hand. You've effectively already done so. Or, you
can try to troubleshoot an unfortunately cryptic error message.
-Justin
Regards
Vinoth
On Mon, Dec 20, 2010 at 11:01 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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
[ 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:
-------------------------------------------------------
There is something wrong with the format of your .rtp file.
Unfortunately, the error message in this case is not particularly
helpful.
Based on the residue and atom naming, it appears that you're trying
to interface some sort of PRODRG output with OPLS-AA. Doing so is
fundamentally flawed, mostly because PRODRG gives GROMOS-compatible
topologies (often poor ones, at that). Presumably, you have
introduced new atom types (opls_966/967) corresponding to some
united-atom C type. OPLS-AA is an all-atom force field, so
introducing a united-atom hexane topology is simply wrong, unless
you have somehow demonstrated that a united-atom model behaves
properly and you have done the thorough work of parameterizing this
model.
-Justin
Regards
Vinoth
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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