AMBER Archive (2006)

Subject: Re: AMBER: antechamber

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Wed Jun 07 2006 - 11:31:46 CDT

antechamber can read gaussian output file directly.
Try to use it without extracting ESP.

On 6/7/06, Steve Seibold <seibold_at_chemistry.msu.edu> wrote:
>
>
>
> I am attempting to generate lipid parameters using Antechamber. leaprc.gaff
> does appear to contain all force field parameters and so no apparent
> problems here. However, when I tried to calculate atomic charges, I started
> running into problems. When using :
>
>
>
> Antechamber -i LIP2.pdb –fi pdb –o LIP2 -fo perpi –nc 0 –c bcc
>
>
>
> I get an error message in my divcon.out saying "Program terminated due to
> errors" I have attached the file (divcon.out) along with my pdb file.
> However, it still assigned charges in my perpi output file. I believe the
> perpi charges (i.e. ANTECHAMBER_PREP.AC) are library values from AMBER
> correct? I also got assigned charges AM1BCC.
>
>
>
>
>
> I also attempted to use "resp". So, I used Gaussian to generate an output
> file (pop=mk) and then used "espgen" to extract ESP information. However
> when I ran:
>
>
>
> Antechamber –I LIP2.ESP –fi gout –o LIP2 –fo perpi –nc –c resp
>
>
>
>
>
> It appears to run, but I am suspicious. I let it run for 70 minutes and
> still no print out …..nothing. So I killed it.
>
>
>
> Does anyone know what I am doing wrong?
>
>
>
> Thanks, Steve
>
>
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> 

-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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