Hi Dupradeau
I have been trying to compute RESP charges using
GAMESS via RED for a modified aminoacid in a huge
biomolecule. The amino acid is carboxy terminal CYS
(or CCYS in AMBER8). An acetyl (ACE) group is linked
to the N end and a Copper (CU+2) atom is attached to
the sulfer atom of the thiol end (SH).
I have pasted my PDB input below. I looks like I have
no problem with naming atoms and connectivity
assignments. I also defined ' CU="29" 'at the end of
RED.pl file. My problem is with the charge of the
molecule. Copper is supposed to have +2 charge. CCYS
has a -1 charge. Together with CCYS(-1) and CU(+2),
the new molecule (CYC) should have a net charge of +1.
When I set the total charge to be +1 in RED.pl, then I
get an error message in GAMESS's output log saying
that the charge is +1 but multiplicity is 1 as well.
Then the GAMESS job gets killed.
When I set the total charge to be 0 in RED.pl (that
is, CU is +1), then GAMESS is OK with that and it
converges the modified aminoacid well.
It seems like GAMESS assigns only +1 charge to the
Copper ion.
Is there any way that I could possibly tell GAMESS or
RED to assign +2 charge to the Copper ion so that
GAMESS does not complain anymore?
regards,
jenk
REMARK REORIENT 16 9 11 | 11 9 16 | 1 7 9 | 9 7 1
REMARK REORIENT 1 9 16 | 16 9 1 | 1 9 11 | 11 9 1
ATOM 1 CT1 ACE 1 2.000 2.090
0.000 1.00 0.00
ATOM 2 H1 ACE 1 2.000 1.000
-0.000 1.00 0.00
ATOM 3 H1 ACE 1 1.486 2.454
0.890 1.00 0.00
ATOM 4 H1 ACE 1 1.486 2.454
-0.890 1.00 0.00
ATOM 5 C2 ACE 1 3.427 2.641
-0.000 1.00 0.00
ATOM 6 O3 ACE 1 4.391 1.877
-0.000 1.00 0.00
ATOM 7 N4 CYC 2 3.555 3.970
-0.000 1.00 0.00
ATOM 8 H4 CYC 2 2.733 4.556
-0.000 1.00 0.00
ATOM 9 C5 CYC 2 4.853 4.614
-0.000 1.00 0.00
ATOM 10 H6 CYC 2 5.408 4.316
0.890 1.00 0.00
ATOM 11 CT7 CYC 2 5.661 4.221
-1.232 1.00 0.00
ATOM 12 H7 CYC 2 5.809 3.141
-1.241 1.00 0.00
ATOM 13 H7 CYC 2 5.123 4.521
-2.131 1.00 0.00
ATOM 14 S8 CYC 2 7.311 4.953
-1.366 1.00 0.00
ATOM 15 H9 CYC 2 7.629 4.369
-2.518 1.00 0.00
ATOM 16 C10 CYC 2 4.713 6.129
0.000 1.00 0.00
ATOM 17 O11 CYC 2 3.601 6.653
0.000 1.00 0.00
ATOM 18 O12 CYC 2 5.709 6.848
-0.000 1.00 0.00
ATOM 19 CU13 CYC 3 8.186 4.423
-0.269 1.00 0.00
CONECT 1 2 3 4 5
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1 6 7
CONECT 6 5
CONECT 7 5 8 9
CONECT 8 7
CONECT 9 7 10 11 16
CONECT 10 9
CONECT 11 9 12 13 14
CONECT 12 11
CONECT 13 11
CONECT 14 11 15 19
CONECT 15 14
CONECT 16 9 17 18
CONECT 17 16
CONECT 18 16
CONECT 19 14
MASTER 0 0 0 0 0 0 0 0 19 0
19 0
END
--- FyD <fyd.u-picardie.fr> wrote:
>
> Difficult to answer without the data. I you agree to
> send me your data, I would
> be very interested to look at what you got...
>
> As I said previously, adding restraints can generate
> very weird charge values...
> The fact that all is done automatically in R.E.D.
> allows to study this problem
> more easily: We will work on this particular problem
> with the handling of
> intra-molecular restraints in R.E.D. III to make the
> detection of these types
> of problems more simple. Regards
>
> F.-Y. Dupradeau
> DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
> The Scripps Research Institute, La Jolla, CA, USA
> --
> http://www.u-picardie.fr/labo/lbpd/FyD.htm
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Received on Sat Mar 12 2005 - 12:53:01 PST
