Dear Ayesha,
vacation time... ;-)
> 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.
ok
> 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?
... 'used' by what?
-1 a PDB file is the input file format required by the Ante_R.E.D. program
-> Ante_R.E.D. generates P2N file(s) from PDB file(s)
-2 a P2N file is the input file format required by the R.E.D. program
-> R.E.D. (versions III.x or IV written using PERL) generates mol2
file(s) from P2N file(s)
-3 mol2 file(s) are loaded in the LEaP program and used as force
field libraries
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
The Cart. coordinates in the R.E.D. input(s) (P2N file) and output(s)
(mol2 file) are different because structures involved in charge
derivation are optimized by using a QM program.
> 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.
oh oh... Only our R.E.D. Python code, which is _not_ yet distributed,
performs atom typing, handles extra-point & united carbon atoms and
generates frcmod files (new modules are currently developed).
R.E.D. Python will be first open to all through R.E.D. Server
Development at
http://q4md-forcefieldtools.org/REDS-Development/ by
the month of September/October 2013. Until that time you could request
a private assistance (see
http://q4md-forcefieldtools.org/REDS/faq.php#5) and we can
post-process the data you generated using R.E.D. Server/R.E.D. Perl
with R.E.D. Python.
> 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.
See once again
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
You have to load the mol2 files in the LEaP program...
- if you used R.E.D. perl you need to define atom types
- if we post-process your data the atom types are defined
> 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.
prepin, off and mol2 (mol3) file formats have all the same role: to be
used as a force field library file format
see
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
> 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?
difficult to answer here - using NMR restraints during MD simulations
and performing equilibration with these restraints might help to
stabilize what you guess is correct...
regards, Francois
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Received on Thu Aug 08 2013 - 03:30:02 PDT
