Hi Martin,
I am running the MCPB program from AMBER tools installed on High
Performace Computer. It has Linux OS with gcc compiler.
gcc version 3.4.6 20060404 (Red Hat 3.4.6-8)
https://docs.loni.org/wiki/About_Linux_x86_Clusters
Thanks,
Naveen Samala
On Thu, May 5, 2011 at 3:01 PM, Martin Peters <martin.b.peters.me.com>wrote:
> Hi Naveen,
>
> Can you tell us what system you are running on (OS/compiler)?
>
> The '-4' value is correct for mtkpp xml files but the "13324544" value is
> not correct.
> I will track down the error as soon as possible.
>
> Regards,
>
> Martin.
>
> On 5 May 2011, at 16:53, Naveen Samala wrote:
>
> > 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
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Thanks,
> > Naveen Samala
> > <1AMP_OH_chg2.xml1>_______________________________________________
> > AMBER mailing list
> > 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 - 13:30:03 PDT
