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>_______________________________________________
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Received on Thu May 05 2011 - 08:30:02 PDT
