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Hi, Anton.<br>
<br>
Thank you for your reply. I looked around for the conversion script you
mentioned, but I only found the following package among the Contributions:<br>
<br>
<b>ConvertGromos2Gromacs</b><br>
This is a program to convert GROMOS96 formatted topology, and conformation
files to their GROMACS equivalents.<br>
Uploaded 19:41 January 10, 2003 by Claudio M. Soares<br>
<br>
I don't think that this is the script you were referring to, because I
installed it and it seems to only be able to convert Gromos 96 topologies
to Gromacs. <br>
<br>
I also found renumtop contributed by you, but there is no documentation
except one gmx-user post. I tried it on an itp file created by PRODRG, but
it returned the same atom types. Either that is not the script you had in
mind or I am doing something wrong. <br>
<br>
Could you give me the name of your script, or perhaps send it to me along
with some information on how to use it to convert an ffgmx itp file to the
ffG43a1 topology?<br>
<br>
Thanks.<br>
<br>
Martina<br>
<br>
Anton Feenstra wrote:<br>
Martina Bertsch, PhD wrote: <br>
<br>
<blockquote type="cite">Greetings. <br>
<br>
I would like to refine Autodock3 results of docking a nonpeptidic indolic
ligand to a membrane receptor model. Because it is computationally expensive
to simulate receptors in the membrane (the 5-ns position restrained MD
to relax the POPC takes me ~ 20 days), I would like to use MD or simulated
annealing in vacuum for some intermediate refinement steps. <br>
<br>
I can generate the protein gro file suitable for vacuum simulations by
selecting the ffG43b1 parameter set in pdb2gmx. But, how do I generate
the ligand gro and itp consistent with this forcefield? I tried using the
ffgmx version of the ligand (as created in PRODRG) and editing the vacuum
ff to include the atomtypes, but somehow that does not seem like the right
thing to do. <br>
</blockquote>
<br>
No, you cannot mix atom types from different forcefields. So, instead <br>
you must choose appropriate 'ff43a1' atom types for your ProDrg generated
<br>
'ffgmx' topology. Also, you will need to select appropriate 'ff43a1' types
<br>
for all bonds, angles, dihedrals and impropers (that is the way it must
be <br>
done in the Gromos forcefield). IIRC, I posted a script to the list (or
<br>
the contributions page), that will replace atom numbers in your .itp/.top
<br>
file by labels that include the atom type, as well as another script that
<br>
does the opposite. Having atom type info in stead of atom numbers makes
<br>
choosing bond-, angle- and dihedral-types so much easier. If you cannot
<br>
find these scripts, please ask me. <br>
<br>
<blockquote type="cite">Which energy groups do I specify for monitoring
to estimate the receptor-ligand binding energy: protein and drg or protein_drg?
<br>
</blockquote>
<br>
protein and drg
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