Hi Martin,
There are no errors found in the log files.
>From the file 1AMP_OH_chg2.prep, the (n-1) residue main chain atom is
missing (it should have been -M).
IMPROPER
CA N H
CA +M C O
CB OD1 CG OD2
IMPROPER
-M CA N H
CA +M C O
CB OD1 CG OD2
You suggested to replace -M with 'N', then what atom I can replace with +M
atom.
IMPROPER
N CA N H
CA +M C O
CB OD1 CG OD2
Also, in the attahced file "1AMP_OH_chg2.xml", the Atom1 number shown
below is generated ambiguous. See also Atom2="-4".
<improper Atom1="13324544" Atom2="3" Atom3="1" Atom4="2" />
<improper Atom1="3" Atom2="-4" Atom3="11" Atom4="12" />
<improper Atom1="5" Atom2="9" Atom3="8" Atom4="10" />
Thanks,
Naveen Samala
On Thu, May 5, 2011 at 10:22 AM, Martin Peters <martin.b.peters.me.com>wrote:
> Hi Navee,
>
> Somehow the improper lines have only three items and they should have four.
>
> The lines:
> CA N H
> should be replaced with:
> N CA N H
>
> Could you search for errors in the *.bcl.log files (grep -i error
> *.bcl.log) ?
>
> Regards,
>
> Martin.
>
> On 5 May 2011, at 15:52, Naveen Samala wrote:
>
> > 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
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Thanks,
> > Naveen Samala
> > <1AMP_OH_chg2.prep>_______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks,
Naveen Samala
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Received on Thu May 05 2011 - 09:00:03 PDT
