Francesco,
> In the meantime, I have taken charges and radii for CONH2 from GLN or
> ACN (which are identical) in the Amber 84 DOT2 database, replacing, or
> attaching to, the charges and radii for PHE from the same database in
> order to get the new residue phenylalanine amide, called PHA. This is
> what I got:
>
> PHA N -0.520 0 0 1.515
> PHA H 0.248 0 0 0.891
> PHA CA 0.214 0 0 1.648
> PHA CB 0.038 0 0 1.711
> PHA CG 0.011 0 0 1.648
> PHA CD1 -0.011 0 0 1.648
> PHA CE1 0.004 0 0 1.648
> PHA CZ -0.003 0 0 1.648
> PHA CE2 0.004 0 0 1.648
> PHA CD2 -0.011 0 0 1.648
> PHA C 0.675 0 0 1.648
> PHA O -0.470 0 0 1.425
> PHA N -0.867 0 0 1.515
> PHA H1 0.344 0 0 0.891
> PHA H2 0.344 0 0 0.891
Do you mean you took the CONH2 group of the side chain of GLN and use
it for the backbone capping group CONH2???
You need a total charge for each amino-acid fragment that has an
integer value.
For sure the NH2 fragment I sent you has a total charge = 0 (+/- .000x)
I am not sure that following your approach leads to an integer total charge:
-0.867+0.344+0.344 = 0.179 !...?
> DOT2 only needs polar hydrogens at this stage. Forget about the 4th
> and 5th column. Is this trivial approach sound? The residue should
> have total charge zero. Not yet checked and not yet tried with DOT2.
>
> As to Firefly, I have some vague remembrance. Is that a new name for
> the diverged GAMESS?
http://classic.chem.msu.su/gran/gamess/index.html
> If so, we are at GAMESS US because the main use I
> made of such programs is for the most complete CASS. GAMESS US was
> second choiche (1st choice MOLCAS but too expensive for us), while the
> diverged gamess did not offer cass, at least at those times. Also,
> extension to Microsoft was of no interest to us at the Accademia
> because the cluster is Linux amd64 Debian.
GAMESS & PC-GAMESS/Firefly lead to identical RESP charge values.
regards, Francois
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Received on Fri Sep 03 2010 - 11:30:03 PDT
