Hi Martin,
Please find the attached file.
Thanks,
Naveen Samala
On Thu, May 5, 2011 at 3:27 AM, Martin Peters <martin.b.peters.me.com>wrote:
> Hi Navee,
>
> Could you send us the 1AMP_OH_chg2.prep file to allow us debug the issue
> you're having?
>
> Regards,
>
> Martin.
>
> On 4 May 2011, at 21:47, Naveen Samala wrote:
>
> > Hi,
> >
> > I am getting the following error when I tried to load the
> > 1AMP_OH_chg2.prep file in x-leap. I have generated the 1AMP_OH_chg2.prep
> > file by running the script 1AMP_OH_toAmberFormats_sem.bcl in MCPB. Can
> you
> > please help me where I did wrong?
> >
> > Welcome to LEaP!
> > Sourcing:
> >
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/dat/leap/cmd/oldff/leaprc.ff94
> > Log file: ./leap.log
> > Loading parameters:
> >
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/dat/leap/parm/parm94.dat
> > Reading title:
> > PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy
> > progs
> > Loading library:
> >
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/dat/leap/lib/all_nucleic94.lib
> > Loading library:
> >
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/dat/leap/lib/all_amino94.lib
> > Loading library:
> >
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/dat/leap/lib/all_aminoct94.lib
> > Loading library:
> >
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/dat/leap/lib/all_aminont94.lib
> > Loading library:
> >
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/dat/leap/lib/ions94.lib
> > Loading library:
> >
> /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/dat/leap/lib/solvents.lib
> >> ZNMP= loadamberprep 1AMP_OH_chg2.prep
> > Loading Prep file: ./1AMP_OH_chg2.prep
> > ** got 3 atoms from IMPROPER line ( CA N H
> > ) - expected 4 (skipping line)
> > ** got 3 atoms from IMPROPER line ( CA N H
> > ) - expected 4 (skipping line)
> > ** got 3 atoms from IMPROPER line ( CA N H
> > ) - expected 4 (skipping line)
> > ** got 3 atoms from IMPROPER line ( CA N H
> > ) - expected 4 (skipping line)
> > ** got 3 atoms from IMPROPER line ( CA N H
> > ) - expected 4 (skipping line)
> >>
> >>
> >>
> >
> >
> > Thanks,
> > Naveen Samala
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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>
--
Thanks,
Naveen Samala
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Received on Thu May 05 2011 - 08:00:02 PDT
