Hello,<br><br>****************output.pdb2gmx is giving Fatal error:<br>Fatal error:<br>
Residue '' not found in residue topology database. Do I need to add Hexane topology to rtp file in library?! Please see below. Thank you very much.<br><br>********************************************************************************<br>
<br>Opening library file ffoplsaa.rtp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat<br>Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat<br>Opening library file /chem_soft/gromacs/share/gromacs/top/atommass.dat<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/vdwradii.dat<br>Opening library file /chem_soft/gromacs/share/gromacs/top/dgsolv.dat<br>Opening library file /chem_soft/gromacs/share/gromacs/top/electroneg.dat<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/elements.dat<br>Opening library file /chem_soft/gromacs/share/gromacs/top/xlateat.dat<br>26 out of 26 lines of xlateat.dat converted succesfully<br>All occupancy fields zero. This is probably not an X-Ray structure<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.atp<br>^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtomtype 1^MAtom$<br>
Opening library file ffoplsaa.rtp<br>^MResidue 1^MResidue 2^MResidue 3^MResidue 4^MResidue 5^MResidue 6^MResidue 7^MResidue 8^MResidue 9^MResidue 10^MResidue 11^MResidue 12^MResidue 13^MResidue 14^MResidue 15^MR$<br>Sorting it all out...<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.hdb<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa-n.tdb<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa-c.tdb<br>
<br>Back Off! I just backed up Hexane-PRODRG.top to ./#Hexane-PRODRG.top.1#<br>There are 0 donors and 0 acceptors<br>There are 0 hydrogen bonds<br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.0.7<br>
Source code file: resall.c, line: 426<br><br>Fatal error:<br>Residue '' not found in residue topology database<br><br>-------------------------------------------------------<br><br>"This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)<br>
<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>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>Entries in vdwradii.dat: 28<br>Entries in dgsolv.dat: 7<br>Entries in electroneg.dat: 71<br>Entries in elements.dat: 218<br>Reading Hexane-PRODRG.pdb...<br>
Read 20 atoms<br>Analyzing pdb file<br>There are 1 chains and 0 blocks of water and 1 residues with 20 atoms<br><br> chain #res #atoms<br> 1 'H' 1 20<br><br>Reading residue database... (ffoplsaa)<br>Processing chain 1 'H' (20 atoms, 1 residues)<br>
<br><br><br><br><br><br>Moeed wrote:<br>
> Hello,<br>
><br>
> I am trying to generate gro and top file with pdb2gmx program. I have<br>
> made a copy of ffoplsaa.rtp from library to working directory and added<br>
> Hexane molecule residue to the beginning of the ffoplsaa.rtp.<br>
<br>
<snip><br>
<br>
>I type in:<br>
><br>
><br>
> pdb2gmx -f Hexane-PRODRG.pdb -o Hexane-PRODRG.gro -p Hexane-PRODRG.top<br>
> -ff oplsaa >& output.pdb2gmx<br>
><br>
<br>
In principal, this should work, but if it's not, then stop redirecting your<br>
output (i.e., let it print to the screen) and see what pdb2gmx is doing.<br>
Otherwise, inspect this "output.pdb2gmx" for error messages, etc.<br>
<br>
-Justin<br>
<br>
> I do not get gro file at all and top file I get contains the following<br>
> comments only!:<br>
><br>
> ;*****************************<div id=":zg" class="ii gt">***************************************<br>
> ; File 'Hexane-PRODRG.top' was generated<br>
> ; By user: moeed (500)<br>
> ; On host: moeed-desktop<br>
> ; At date: Sun May 9 10:47:26 2010<br>
> ;<br>
> ; This is your topology file<br>
> ; "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)<br>
> ;<br>
> ; Include forcefield parameters<br>
> #include "ffoplsaa.itp"</div>