Dear Karl and Dan,
Jobs are still running but preliminary results show the charges on
these terminal C-H carbon and hydrogen atoms are not that close to
zero... So one can imagine what would the results if this molecule
would be functionalized by a heterocyclic group or even some alkyl
groups...
regards, Francois
Quoting FyD <fyd.q4md-forcefieldtools.org>:
> Dear Karl,
>
> It looks like my answer was not delivered: see this answer below....
>
> regards, Francois
>
> ----------------------------------------------------------------------------
>
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> Re: [AMBER] Graphene topology from GAFF
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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 Wed Jun 26 2013 - 02:30:02 PDT
