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
>
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> 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 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu