AMBER Archive (2006)

Subject: Re: AMBER: Gaussian, antechamber, RESP

From: Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Stefano.Pieraccini_at_unimi.it)
Date: Sun Sep 03 2006 - 07:57:57 CDT

Have you added the flag -nc 'molecular net charge with sign' in the antechamber command line? The default for the molecular charge is 0.

Best Regards

Stefano Pieraccini

----- Messaggio Originale -----
Da: Ed Pate <pate_at_math.wsu.edu>
Data: Domenica, Settembre 3, 2006 12:03 am
Oggetto: AMBER: Gaussian, antechamber, RESP
A: amber_at_scripps.edu

> Dear Amber community:
>
> I am trying to use Gaussian and RESP to develop charges and a
> prep file for ATP.
> I am using ATP as a test example since I already have such a
> file. I am using
> the antechamber protocol described at
> http://amber.scripps.edu/Questions/mail/107.html, suggested by
> David Case. I am
> using Amber 7 on the Xeon cluster at NCSA. Things are not
> working and I
> am hoping someone can point me in the right direction.
>
> I develop a pdb file for ATP (atp.pdb) using an ATP structure
> from the protein
> data bank and tleap to add hydrogens.
>
> I then use the command
>
> antechamber -i atp.pdb -fi pdb -o atp.com -fo gcrt
>
> The antechamber output is edited to generate the following
> atp.com file for input
> into Gaussian:
>
> %chk=atp
> %Nproc=2
> %Mem=1GB
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
>
> antechamber for atp
>
> -4 1
> O
> 35.7900 61.2270 54.3480
> P
> 36.8540 61.3650 55.3620
> (rest of ATP molecule follows)
> space in cc1 of the last line
>
> Gaussian03 is then run. Gaussian98 is not available.
> Convergence is achieved.
> The Gaussian output is in atp.out.
>
> I then run
>
> antechamber -i atp.out -fi gout -o atp.prepi -fo prepi \-c resp -
> s 2
>
> The files ANTECHAMBER_RESP1.IN, ANTECHAMBER_RESP1.OUT,
> ANTECHAMBER_RESP2.IN/OUT,atp.prepi, etc. are generated.
> However, antechamber is not picking up the
> correct individual atom charges for ATP or the -4 total charge
> of the molecule
> (charge=0 instead).
>
> I would greatly appreciate it if someone could help me
> understand what is going
> wrong and how to fix things.
>
> Thanks,
>
> Ed Pate
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