The outcome of MD was most disappointing, and a remedy applied most
intriguing.
The largest ligand had been optimized, and no negative frequencies arose
(Gaussian at the computer center). The gaussian log gave the RESP partial
charges and mol2 on the PyRED server. Minimization (NAMD 2.10, water box,
neutralized), even at timestep 0.001, caused a vast deformation of one of
the three cycles (the one bearing N-CO-NH that I discussed before), and of
the C-O-P angle (phosphate phosphorus). Gradual heating to 300k with
timestep 0.001 did not correct the structure. Very good parmchk2 score
notwithstanding, I had to conclude that the parameterization by analogy
(antechamber parmchk2) was no good.
Intriguing is the following, from attempts after the above runs. A simple
antechamber run from the X-ray diffraction above said structure (H added
with chimera), followed by charmmgen, gave rtf/prm files (amd1 partial
charges). From these, vmd gave psf/pdb files that allowed minimization
(NAMD 2.10, water box, neutralized) at timestep 1.0 without structure
deformation. The same on heating to 300K at timestep 1.0.
It seems that I did something wrong with amber, however I used conf files
that I had used before successfully on running amber on namd (and which
account for all suggested
http://ambermd.org/namd/namd_amber.html
In fact, the smaller ligand, p-hydroxyphenylacetate (treated as above, QM
optimization, PyRED server) was dealt with correctly along amber/namd.
francesco pietra
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret.gmail.com>
Date: Sun, Sep 20, 2015 at 4:47 PM
Subject: Re: [AMBER] q4md FF with two "small" molecules
To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org>
Dear Professor Case:
Use LEaP to read in the mol2 or off files you create for each ligand
> separately; load the corresponding frcmod files (if any); load a pdb file
> with the protein + both ligands; output a parm7/rst7 combination that has
> everything. Give that to NAMD, paying attention to the instructions here:
>
> http://ambermd.org/namd/namd_amber.html
>
thanks a lot for such a concise, clear guidance. My memory was obstructed
by the long use of xplor (albeit no good excuse). Actually, I had learned
from Professor Dupradeau long ago how to set up the above with LEaP, and in
a more complex case, involving bonding between ligands and the protein,
which I could carry out successfully. I'll try that now with the new
ligands/proteins. As the latter is very large, first with the ligands only,
to check their stability under MD, as their FF was built by analogy.
francesco
On Sun, Sep 20, 2015 at 2:40 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Sun, Sep 20, 2015, Francesco Pietra wrote:
> >
> > My aim is to get the FF for a protein bearing the two ligands. As far as
> I
> > know leap does not read parm7/rst. Also, as far as I know, running
> > parm7/rst with NAMD (which I intend to do, having no recent amber
> version,
> > nor money for that) requires a single parm7/rst.Thanks for suggesting a
> > procedure.
>
> Use LEaP to read in the mol2 or off files you create for each ligand
> separately; load the corresponding frcmod files (if any); load a pdb file
> with the protein + both ligands; output a parm7/rst7 combination that has
> everything. Give that to NAMD, paying attention to the instructions here:
>
> http://ambermd.org/namd/namd_amber.html
>
> ...good luck....dac
>
>
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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 21 2015 - 03:30:03 PDT
