Dear Karl,
It looks like my answer was not delivered: see this answer below....
regards, Francois
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----- Forwarded message from fyd.q4md-forcefieldtools.org -----
Date: Wed, 19 Jun 2013 16:56:53 +0200
From: FyD <fyd.q4md-forcefieldtools.org>
Reply-To: FyD <fyd.q4md-forcefieldtools.org>
Subject: Re: [AMBER] Graphene topology from GAFF
To: AMBER Mailing List <amber.ambermd.org>
Cc: "Karl N. Kirschner" <kkirsch.scai.fraunhofer.de>,
fan.wang.q4md-forcefieldtools.org, jpb.q4md-forcefieldtools.org,
cieplak.cgl.ucsf.edu
Dear Karl,
Antechamber was_?/was not able, and then was able to handle chemical
equivalencing for 'classical' molecular systems, and does not handle
systems such CNT, fullerene, etc... Ante_R.E.D. 1.x does not handle
chemical equivalencing between different chemical groups, while
Ante_R.E.D. 2.0 does with limitations (2.0 does not handle
long/repetitive chains, CNT, fullerenes...). All that has to be
clearly defined for users. More recently, we have developed a new
algo. for chemical equivalencing within R.E.D. Python, which should
handle complex cases such as CNT, fullerene, graphene...
I agree with your point about charge derivation of molecules with a
small dipolar moment. A good/simply example is dihydrogen. Other
tricky cases are some alkanes (but not all).
The approach we have developed in R.E.D. Python does handle CNT,
fullerene, graphene, which include 'regular' structures (with charges
close to zero as you underlined), but also functionalized versions,
where the charges of the incorporated chemical groups are all but
zero: what about a fullerene or a CNT with an epoxyde group for
instance? In such a polymer where do you start to have zero charges
and non-zero charges? Our algo. does answer to this type of problem
(besides that of alkanes).
We will release some of these results in R.E.DD.B. soon, and plan to
open R.E.D. Python to all through 'R.E.D. Server Development' by
September 2013.
regards, 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.
----- End forwarded message -----
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Received on Thu Jun 20 2013 - 07:30:02 PDT
