Hi Justin<br><br>I had taken United atom pdb file form PRODRG and i want to use OPLS-UA force field. i dont know what's wrong out there.I have done it befor for other molecules like DCE, CCL4 etc.<br><br>Regards<br>Vinoth<br>
<br><div class="gmail_quote">On Mon, Dec 20, 2010 at 11:01 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5"><br>
<br>
vinothkumar mohanakrishnan wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all<br>
<br>
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<br>
<br>
[ DRG ]<br>
[ atoms ]<br>
CAA opls_966 0 1<br>
CAF opls_966 0 1<br>
CAB opls_967 0 2<br>
CAC opls_967 0 2<br>
CAD opls_967 0 2<br>
CAE opls_967 0 2<br>
[ bonds ]<br>
CAA CAB<br>
CAB CAC<br>
CAC CAD<br>
CAD CAE<br>
CAE CAF<br>
[ angles ]<br>
CAA CAB CAC<br>
CAB CAC CAD<br>
CAC CAD CAE<br>
CAD CAE CAF<br>
[ dihedrals ]<br>
CAA CAB CAC CAD<br>
CAB CAC CAD CAE<br>
CAC CAD CAE CAF<br>
<br>
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 (<a href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html" target="_blank">http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html</a>) previously i used pdb2gmx for other molecules and it worked fine for the oplsaa force field. any help is highly appreciated.<br>
<br>
Opening library file ffoplsaa.rtp<br>
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>
WARNING: masses will be determined based on residue and atom names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat<br>
Entries in atommass.dat: 178<br>
WARNING: vdwradii will be determined based on residue and atom names,<br>
this can deviate from the real mass of the atom type<br>
Opening library file vdwradii.dat<br>
Entries in vdwradii.dat: 28<br>
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat<br>
Entries in dgsolv.dat: 7<br>
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat<br>
Entries in electroneg.dat: 71<br>
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat<br>
Entries in elements.dat: 218<br>
Reading hexane.pdb...<br>
Read 6 atoms<br>
Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat<br>
26 out of 26 lines of xlateat.dat converted succesfully<br>
Analyzing pdb file<br>
There are 1 chains and 0 blocks of water and 1 residues with 6 atoms<br>
<br>
chain #res #atoms<br>
1 ' ' 1 6 <br>
All occupancies are one<br>
Opening library file ffoplsaa.atp<br>
Atomtype 1<br>
Reading residue database... (ffoplsaa)<br>
Opening library file ffoplsaa.rtp<br>
<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.0.7<br>
Source code file: resall.c, line: 279<br>
<br>
Fatal error:<br>
in .rtp file at line:<br>
<br>
<br>
-------------------------------------------------------<br>
<br>
</blockquote>
<br></div></div>
There is something wrong with the format of your .rtp file. Unfortunately, the error message in this case is not particularly helpful.<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Regards<br>
Vinoth<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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