Dear Karl,
Attached you will find a tar.gz file with the graphene setup you are
asking for. However, you might complaint about the charges I used but let
me cite Lewis Carroll in "Alice in Wonderland":
"Alice: Would you tell me, please, which way I ought to go from here?
The Cheshire Cat: That depends a good deal on where you want to get to.
Alice: I don't much care where.
The Cheshire Cat: Then it doesn't much matter which way you go.
So, if your sistem is supposed to be a "toy model", it doesn't much matter
which charge scheme you use.
Best wishes,
Hector.
> 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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--------------------------------------
Dr. Hector A. Baldoni
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4423789 ext. 157
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Received on Tue Jun 18 2013 - 15:00:02 PDT
