AMBER Archive (2009)

Subject: [AMBER] gaussian 98 input/output for antechamber/resp

From: wong105_at_llnl.gov
Date: Wed Aug 12 2009 - 13:41:45 CDT

Dear Amber users;

     I'm using antechamber (Amber 8)/gaussian 98 to calculate charges
for a ligand. I start with a mol2 file and obtain from antechamber a
gaussian input file. The gaussian input file looks like this:

--Link1--
%chk=MOL
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt

remark line goes here

1 1
     N 1.2410 -4.7650 42.5820
     C 0.1340 -4.4500 43.3000

I made the assumption that I could take this input file to obtain the
electrostatic potential for RESP. I also noticed the "opt" keyword,
which, I assumed served the purpose of relaxing the molecule to obtain
a reasonable response.

Two observations:

1) I noticed that the electrostatic potential data is only printed
for the first point in the optimization, rather than the final
geometry. That would seem to defeat the point of the optimization.

2) After 10,000 points, one gets **** for the point number:

       ESP Fit Center 9998 is at -1.493521 -3.825592 -3.033347
       ESP Fit Center 9999 is at -1.062486 -3.825592 -3.033347
       ESP Fit Center **** is at -0.657445 -3.678169 -3.033347
       ESP Fit Center **** is at -0.327253 -3.401105 -3.033347
       ESP Fit Center **** is at -0.111735 -3.027817 -3.033347

Does the resp program know how to deal with this? It does not yield
show any errors when I run it to calculate charges, but I wonder if it
ignores these points. Perhaps others have addressed these points in
the past, but a quick google search did not yield an obvious answer.
Any ideas?

Thanks;

-Sergio

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