Dear Hector,
Thank you very much for your help and the files (and for reminding me of the
Cheshire Cat). It's good to see what the molecule looks like in Mol2 format.
I will still try to see if I can find a way to assign the partial charges
but regardless, it's good to finally be able to run a simulation.
Sincerely,
Dan
-----Original Message-----
From: Hector A. Baldoni [mailto:hbaldoni.unsl.edu.ar]
Sent: Tuesday, June 18, 2013 2:40 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Graphene topology from GAFF
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 - 17:30:02 PDT
