Re: AMBER: frcmod

From: David A. Case <>
Date: Mon, 18 Jun 2007 12:37:52 -0700

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 errors
from 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.)


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Received on Wed Jun 20 2007 - 06:07:26 PDT
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