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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 18 2013 - 00:30:02 PDT
