shahrbanoo karbalaee wrote:
Dear justin
I want to creat topology file tfe by ffopls.I get pdb file tfe and add
atoms and bond tfe atoms to ffoplsrtp file in top file gromacs.so in
hdd I add hydrogen atoms.when I do pdb2gmx -f tfe.pdb.I get this
message:
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp
Residue 56
Sorting it all out...
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.hdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa-n.tdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa-c.tdb
Back Off! I just backed up topol.top to ./#topol.top.8#
Processing chain 1 (9 atoms, 1 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Program pdb2gmx, VERSION 3.3.2
Source code file: resall.c, line: 436
Fatal error:
Residue 'TFE' not found in residue topology database
Then you have done something incorrectly in your creation of the .rtp entry;
probably incorrect naming. If you intend on using TFE as a solvent, it is much
easier to create a simple .itp file for it and #include it in your system
topology. Generally, .rtp entries are building blocks for common macromolecules
(although there are a few exceptions, i.e. NADH, ATP, and a few others commonly
associated with proteins).
-Justin
thank you foe your advise.
karbalaee
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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