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>_______________________________________________
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Received on Thu May 05 2011 - 13:30:02 PDT
