AMBER Archive (2008)


Date: Mon Dec 08 2008 - 12:31:24 CST

Dear community!

I am just beginning to study QM, so I am not an expert. Please be gentle!
I generate RESP charges for a series of ligands using AMBER9.

I follow this procedure:

1) "antechamber -fi pdb -i ligand.pdb -fo gcrt -o -pf no" to generate my input template

2) I edit the gaussian options to: #HF/6-31g* scf=tight test pop=mk iop(6/33=2) iop(6/42=6) opt

To my understanding: 6/42=6 specifies the density points in each layer, 6/33=2 (which is NOT documented in gaussian 03) prints out potential points and potentials. On is is also recommended to use iop(6/41=10) on top, which would add 10 concentric layers of points for each atom. Is this option recommended or is it a carryover?

3) I run Gaussian03 which outputs a ligand.log file

4) I run 'antechamber -fi gout -fo prepi -i ligand.log -o ligand.prepi -c resp -s 2 -pf no'

and voila the resp charges are found in the prepi file. These charges are similar to AM1-BCC (which I suppose they should be as AM1-BCC has been parametrised to reproduce RESP).

To get a feeling of whether this procedure is correct I had a look at /usr/local/amber9/examples/resp_charge_fit/water. I created a water molecule in molden and applied the same procedure (this time with and without option iop(6/41=10)). The obtained charge are basically identical:

O1 -0.81327
H1 0.40664
H2 0.40664

According to /usr/local/amber9/examples/resp_charge_fit/water/* I should get:

O1 -.568182
H1 0.284091
H2 0.284091

Looking at the gaussian optimised geometry of the water molecule I find small deviatons in the angle H1-O1-H2 compared to the standart water angle. What is happening here? Can I trust the RESP charges for my own ligands? Where can I find
more complete examples, other than the ones in /usr/local/amber9/examples/resp_charge_fit/* as they only come with input for resp but no files that have been used before that.

I apologize if the mailing list is not the right place to post. However, I am grateful for any pointers!



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