Thank you Dr. for your response. it helped solve a few queries.
I was finally able to run my complex.
regards
ayesha
On Thu, Aug 8, 2013 at 6:18 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 Sat Aug 10 2013 - 20:00:02 PDT
