AMBER Archive (2008)

Subject: Re: AMBER: help regarding warning message

From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Mar 25 2008 - 15:23:55 CDT

Thank you Dr. Case.

 I was using par99 not par94 file. So with slight modifications in frcmod
file it is working fine.
best regards
s

On Tue, Mar 25, 2008 at 1:51 PM, David A. Case <case_at_scripps.edu> wrote:

> On Tue, Mar 25, 2008, snoze pa wrote:
>
> > I am using amber heme parameter but getting some warning. Do you think
> i
> > should take these warning seriously?
> > thanks for your help.
> > s
> >
> > > loadAmberParams /usr/local/amber9/benchmarks/hb/frcmod.hemall
> > Loading parameters: /usr/local/amber9/benchmarks/hb/frcmod.hemall
> > Reading force field modification type file (frcmod)
> > Reading title:
> > No mass defined for non-bond atom type: LO - skipping
> > No mass defined for non-bond atom type: LC - skipping
> > > loadAmberPrep /usr/local/amber9/benchmarks/hb/heme_all.in
> > Loading Prep file: /usr/local/amber9/benchmarks/hb/heme_all.in
> > (UNKNOWN ATOM TYPE: NO)
> > (UNKNOWN ATOM TYPE: CX)
> > (UNKNOWN ATOM TYPE: CX)
> > (UNKNOWN ATOM TYPE: NO)
> > (no charges read on atoms lines in deoxy Heme residue ALL ATOM,
> Yves
> > names, Bayly-modified)
> > Loaded UNIT: HEM
>
> Well, you can test to see if you get the same prtmop file. The warnings
> above
> look innocuous to me.
>
> ...dac
>
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