Dear All,
Hi. I have just started using the RED server because of my supervisor's
recommendations and several recommendations on the mailing list for adding
the RESP charges on the ligand. I have a small organic molecule taht i have
complexed witha a protein via docking and now i am interested in the MD of
that complex.
I have a few questions which i have not been able to search on the mailing
list most probably because of wrong search string
1. Which file is to be used? According to Tutorial 3 on the RED home page,
the .mol2 file need to be used. When i look at the output, the coordinates
that were given in the p2n file differ from the .mol2 file. I am attaching
both files. Is that normal?
2. On on of the mailing list emails, it was written that i could get the
frcmod files. Which is it on the list of files, as i have no file with the
frcmod extension.
3. when i want to use the mol2 of the RED in amber. what is the correct
procedure as when i run the parmchk command, there are several "Attn: needs
revision" lines. However, if I apply the gaff forcefield on the mol2 file
and then run the parmchk command, no errors are reported.
4. I have another question and that is related to putting charges on the
molecule using antechamber.
Everything goes fine until the prepin file. Upon checking the prepin file,
one of my atoms goes missing, which is a bit confusing. I tried this a few
times with similar results.
5. Another question is related to keeping water in the active sight. When
we do docking, we remove the water. When we want to do MD, some would like
to keep the water in the active sight. what happens if the water molecules
are very near to the binding sight of the ligand. My understanding is that
they will interfere during MD. Is it OK to remove them and keep the
remaining?
Hoping someone may answer soon
Thank you
Regards
Ayesha
PhD candidate
UPM/UM, Malaysia
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: zer31.p2n
Received on Tue Aug 06 2013 - 19:30:02 PDT
