We have found ourselves several times in a situation where we have to parametrize compounds for running MDs.
In this blog entry, I will try to set up a protocol for parametrization of small molecules dihedrals for AMBER using Gaussian and sander (based on the tutorial found in this webpage).

I have recently run into some troubles trying to parametrize a ligand with the latest version of antechamber. As Sergi reported recently, the iop(6/33=2) was deleted in the revision b1 of Gaussian and replaced by the new iop(6/50=1) in the later revision c1 (available at CESCA). The fact is that in the AMBER12 guide is not clearly explained how to obtain an AMBER prep file from the new Gaussian output and for me it has being a little jigsaw. I hope this save you some headaches:

Due to the demand to use the organic/water mixtures published in the MDMix work done in our group, here you can download two preequilibrated boxes:

• ETAWAT20 (ethanol 20% concentration)
• ISOWAT20 (isopropanol 20%). 

These boxes are saved in Amber Object File format. Prepared to work with tLeap or xLeap from Amber software.

      For those who need to parametrize new ligands, there is a new alternative VMD pluggin, named Paratool,  to do so. It works for both AMBER and CHARMM, but has been specially designed for the latter one.

Thanks to Jordi, we could find a solution to this gaussian bug: (I wanted to parametrize a compound with iop(6/33=2) which has been deleted in our marc g09 version)

http://ambermd.org/bugfixesat.html



Gaussian 09 fix

To compile AMBER can be a really hard (or at least long) work. Here there is the list of commands that worked for me in my Snow Leopard machine.  I hope this ease the things a little bit for you.
Enjoy ;-)

rDock is a fast & free docking program designed to be used in High-Throughput Virtual Screening. This is a summary of the steps necessary to do so. You must have previously defined yor system & cavity (consult the manual)

PART 1: DEFINING THE RIGHT PARAMETERS FOR HT-MODE

Start by executing 50 docking runs for a set of ligands representative og your entire collection:

rbdock -i $f -o ${f}_out -r REC.prm -p dock.prm -n 50 > ${f}_out}.log

rDock is a fast & free docking program designed to be used in High-Throughput Virtual Screening. This is a summary of the steps necessary to do so.

1) You mst have previously defined yor system & cavity (consult the manual)

2) Execute 50 docking runs for a set of ligands representative og your entire collection:

rbdock -i $f -o ${f}_out -r REC.prm -p dock.prm -n 50 > ${f}_out}.log

So, your output files are named *_out.sd. Create a report file:

     Sometimes, I've faced the problem to determine the number of contacts between protein residues and a given ligand (which may come from x-ray or docking results).
 

  Googling I found this webpage that could be useful for some people who might start using Gaussian (from very basic to more realistic and complicated cases).

    I only expected could be as useful as it were for me.

    The e-link is:

https://www.wiki.ed.ac.uk/display/EaStCHEMresearchwiki/Training