Re: [AMBER] tinker_to_amber error

From: Ray Luo <rluo.uci.edu>
Date: Mon, 1 Aug 2016 10:40:08 -0700

Xiaoliu,

A common mistake is that a prmtop file and/or an inpcrd file are in
the working directory with the same names. The program won't do
anything if this is the case. Maybe it's better to use the option "-O"
like the sander program. Not sure it's implemented here.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Mon, Aug 1, 2016 at 8:52 AM, Xiaoliu Zhang <xzhan91.lsu.edu> wrote:
> Dear amber user,
>
>
> I'm running tinker_to_amber command following the Amber 16 manual. The system I used to test only has one CH3OH molecule. I have installed the tinker6, and the Amber 16 tool without Amber.
>
>
> First I got my methanol.xyz , methanol.key, and methanol.pdb file. The parameters I was using is amoeba04.prm.
>
>
> Then I ran
>
> $TINKER_HOME/bin/analyze methanol PC > methanol.analout
>
> and it worked.
>
>
> Next, I ran tinker_to_amber command, and it gave me an error:
>
>
> username-PC:~/Documents/ambertest$ tinker_to_amber -name methanol -title "methanol amoeba04 FF"
> cfieldfile = /home/xiaoliu/Documents/ambertest/amoeba04.prm
> trouble opening prmtopfile methanol.prmtop
>
>
> As a result, I only got an empty prmtop file and no inpcrd file.
>
>
> I attached all the files I have. Is there any method to fix this problem?
>
>
> Many thanks!
>
>
> Xiaoliu
>
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Received on Mon Aug 01 2016 - 11:00:03 PDT
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