It works by changing the force field from ff99 to ff99SB. Thanks
Aimin
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Thursday, July 21, 2011 10:09 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command
ff99 is an old force field. I would suggest sourcing ff99SB instead:
xleap -f leaprc.ff99SB
This should load the appropriate FF libs.
HTH,
Jason
On Thu, Jul 21, 2011 at 12:58 PM, Aimin <aimin.guo.csun.edu> wrote:
> I type "$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99" in
> the command line. Then the Xleap window appears. Is that OK? Thanks.
>
> Aimin
>
> ________________________________________
> From: Emmanuel Baribefe Naziga [baribefe.gmail.com]
> Sent: Thursday, July 21, 2011 9:37 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence
> using "sequence" command
>
> Check to see if you sourced the forcefield files before the sequence
> command.
>
> Emmanuel
>
> On Thu, Jul 21, 2011 at 10:28 AM, Aimin <aimin.guo.csun.edu> wrote:
>
> > Dear Amber users,
> >
> > In tutorial B3, when I type TC5b = sequence {NASN LEU TYR ILE GLN TRP LEU
> > LYS ASP GLY GLY PRO SER SER GLY ARG PRO PRO PRO CSER} in Xleap, I met the
> > following problem: "sequence: Illegal UNIT at position #1" and cannot
> create
> > the TC5b amino acid, for whatever the NumLock is turned on or turned off.
> I
> > use Amber 11. Thank you in advance.
> >
> > Aimin
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jul 21 2011 - 10:30:04 PDT
