Dear Karl, Francois, and Dr. Case,
Thank you very much for taking the time to help me. I'm very new to MD and
am still trying to get a grip on the vast amount of material. The system I'm
trying to simulate is a compromise between time and detail (as is all MD, I
suppose). However, this simulation in particular is supposed to be a "toy
model" that determines the value of larger scale simulations. I am examining
the behavior of a previously reported peptide (Naik et al, JACS 2011) and
the influence of certain structural modifications on its tendency to bind
roughly linear edges vs. curved pores. Therefore, my model tries to squeeze
both features into a small topology. Are there better ways to approach the
problem?
Francois, thank you for running my structure through R.E.D. I am very
interested to see the result.
I did find a working method for getting my structure into LEaP: I imported
the PDB into Maestro, saved as a .xyz, opened this xyz in Maestro, and saved
as Mol2 which I could then open in tleap. This combination of operations
enabled the correct determination of bonding and aromaticity; however, I'm
not sure if I can trust the charges. This method was suggested by another
student and I have not yet had a chance to figure out how Maestro assigns
charges. Are there any obvious pitfalls to this method?
Thank you again,
Dan
-----Original Message-----
From: Karl N. Kirschner [mailto:kkirsch.scai.fraunhofer.de]
Sent: Tuesday, June 18, 2013 1:18 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Graphene topology from GAFF
Hi Dan (and Francois),
I'll throw my two cents in. For molecules that do not have a permanent
dipole moment, determining classical atom-centered point charges that are
representative of the quantum charge distribution is difficult to do. As far
as I know, such a problem is still unsolved.
One would have to validate the determined charges (as always) using
experimental/QM observable that is dependent upon the nonbonded forces. The
graphene sheet you attached shows a slight asymmetry in the structure, so it
should have a "very" small permanent dipole. However, I don't think it would
be enough to produce reliable partial atomic charges.
Like Dr. Case mention, the carbon atoms should predominantly have charges
of zero for an large (i.e. infinite) sheet. In your model there are many
carbons that are attached to hydrogen atoms (i.e. a relatively high ratio of
edge-to-embedded carbons compared to reality), which might give rise to
artificial MD behavior due to partial atomic charges and Lennard-Jones
parameters. This would be true if you are trying to model a large sheet.
However, if your model is representative of an experimental structure, then
this would not be the case.
Cheers,
Karl
----- Original Message -----
From: "FyD" <fyd.q4md-forcefieldtools.org>
To: dpiraner.caltech.edu, "fan wang" <fan.wang.q4md-forcefieldtools.org>
Cc: "AMBER Mailing List" <amber.ambermd.org>
Sent: Tuesday, June 18, 2013 9:20:52 AM
Subject: Re: [AMBER] Graphene topology from GAFF
Dear Dan,
I do not think the method of the graphs is suitable to determine chemical
equivalencing here: I would _not_ use Antechamber (from what I understand
more there are cycles more you need memory; the problem you encountered; my
guess is that upgrading to the last version will change nothing) to
determine the charges here, besides the problem related to geometry
optimization.
As underlined by Dr Case the atomic charges of the hydrogen atoms are
supposed to be slightly different; thus I would derive the atomic charges of
this molecule (i.e. I would not set all of them to zero).
I just ran R.E.D. Python on your molecule to test how goes chemical
equivalencing in this case. It should work with our algo. The problem is
that your molecule is quite big for our cluster, and it might take 'some'
time to get an optimized geometry. Then, you will be able to decide if you
want RESP vs ESP; Connolly surface vs CHELPG, etc... The RRMS of the fit is
important in this case; if it is not good we will propose you alternatives
to improve the fit; all that is quite stable in R.E.D. Python by now...
I let you know what we get...
regards, Francois
> I'm trying to obtain .top and .crd files for a graphene sheet using
> AMBERtools 1.4. I generated the graphene pdb file using VMD's nanotube
> builder plugin, and added terminal hydrogens using PyMOL. I then
> replaced the VMD atom names (C and H01) with what I believe to be the
> appropriate GAFF atom names: CA and HA. The structure was then used as
> an input for Antechamber, to be then loaded into tLEaP:
>
> antechamber -i graphene.pdb -fi pdb -o graphene.prepin -fo prepi -c
> bcc -j
> 4 -at gaff
>
> I received a huge amount of warnings from Antechamber about exceeding
> 10 residues, a final warning about reallocating memory due to
> exceeding MAXBOND, and then the program appeared to freeze. I can't
> tell if it's still calculating slowly or simply stuck in a loop.
>
> Is the procedure I'm following correct for defining a graphene molecule?
> Is the format of the PDB file, attached, correct? I wasn't able to
> find much information about the setup online, other than that it has
> previously been done. Any help would be greatly appreciated.
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Received on Tue Jun 18 2013 - 03:00:02 PDT
