AMBER Archive (2007)

Subject: Re: AMBER: frcmod

From: Brooke Elizabeth Adams (badams11_at_mix.wvu.edu)
Date: Mon Jun 18 2007 - 15:02:13 CDT

When looking in xleap, we realized that the gaff.dat params were not
loaded into the program. After fixing this, all was well. Thank you so
much for your help.

Thank you so much for your help.
----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Monday, June 18, 2007 3:39 pm
Subject: Re: AMBER: frcmod
To: amber_at_scripps.edu

> On Mon, Jun 18, 2007, Brooke Elizabeth Adams wrote:
>
> > When using the GAFF, either not included, -at gaff, or -at GAFF, the
> > frcmod output file did not include all the atoms, bonds, or
> information> needed. It was just left blank. I am not sure why it
> did this, however,
> > the problem still lies in finding the relationship of:
> >
> > CZ - P - NT or c1 - p5 - n3, still looking for force numbers
> >
> > (the input file is the same, with the code,
> > antechamber -i tabun_2_A02.pdb -fi pdb -o TAB.prepi -fo prepi -at
> GAFF> -rn TAB -c bcc&
> > (also -at gaff and nothing)
>
> Works for me. I'm assuming that you also ran parmchk(?). Can you
> post the
> actual frcmod file? Note that the frcmod file *should* be mostly
> blank,since almost all the necessary parameters are in gaff.dat.
>
> I am still confused about why you have upper case letters. And,
> how do
> know that these are still needed, or missing? (That is, do you get
> errorsfrom tleap later on? It's certainly conceivable that parmchk
> fails to
> estimate some parameters that are really needed, but we haven't
> seen that sort
> of failure before. This is why we need complete details in order
> to be able
> to try to reproduce the problem here. So, please indicate exactly what
> commands you gave to tleap as well as any output you received.)
>
> ...dac
>
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