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
Received on Thu May 05 2011 - 01:30:02 PDT
