AMBER Archive (2007)

Subject: Re: AMBER: frcmod

From: Brooke Elizabeth Adams (badams11_at_mix.wvu.edu)
Date: Fri Jun 15 2007 - 14:11:00 CDT

Here are the files,
and the command for antechamber

antechamber -i tabun_2_A02.pdb -fi pdb -o TAB.prepi -fo prepi -at AMBER
-rn TAB -c bcc&

parmchk -i TAB.prepi -fi prepi -o TAB.frcmod

I am hoping to find the numbers for the frcmod so that the forces will
be correct.

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Tuesday, June 12, 2007 5:35 pm
Subject: Re: AMBER: frcmod
To: amber_at_scripps.edu

> On Tue, Jun 12, 2007, Brooke Elizabeth Adams wrote:
>
> > In Amber 8, I am working with the molecule Phosphoramidocyanidic
> acid,> dimethyl-,ethyl ester. The parm file, frcmod, does not have
> force field
> > values for some bonds.
>
> We need more information about what you really mean when you say "I am
> working" with a certain molecule. Did you use antechamber? Or get
> the frcmod
> file by some other method? If you used antechamber, please post
> the exact
> command line you used, plus the input pdb file (or whatever was used.)
> If you used some other method, you need to say what that was (and
> why you
> didn't use antechamber.)
>
> >
> > CY - P5- NT
> > nitrile C, P with four bonded atoms, n3
> > and
> >
> > CY -P5 -os
> > nitrile C, P with four bonded atoms, Os
>
> You seem to have a strange mixture of upper-case and lower-case
> atom types,
> and I can't tell how that came about. GAFF would always have all
> lower-case
> atom types.
>
> ...regards...dac
>
> --------------------------------------------------------------------
> ---
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>




  • application/octet-stream attachment: TAB.prepi
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu