On 5/13/12 5:54 AM, Kowsar Bagherzadeh wrote:
Dear Users,
I am trying to generate an *.ITP file for a ligand I am studying using Prodrg
server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar
hydrogens) while the *.ITP file dispays 37 atoms and it does not display the
double bond in the structure, which results in an error in simulation. Other
files that Prodrg gives like DRGAPH.PDB display 37 atoms same as the *.ITP file
and they also do not display the double bond in the structure ! only the
DRGFIN.PDB with 41 atoms ( all hydrogens) displays the double bond. I have used
Prodrg several times before and this is the first time it happens. are there any
other online services or any software for the purpose? Thank you
Whether or not any file "displays" a double bond is irrelevant. There will not
be duplicate bonds in the .itp file, nor will a double bond necessarily appear
in visualization software, though some programs may try to guess.
The most important things to do are obtain the coordinate file that matches the
topology (e.g., the one that does not have nonpolar hydrogens, per Gromos
convention) and realize that you will need to do a fair bit of work to improve
the PRODRG topology: http://pubs.acs.org/doi/abs/10.1021/ci100335w
ATB is another option. It is newer and performs better.
http://compbio.biosci.uq.edu.au/atb/
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
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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