Dear Professor Case,
My initial file
xleap commands
source leaprc.gaff
loadamberparams pmma_3mer.frcmod
x=loadmol2 pmma_500mer.mol2
check x
saveamberparm x pmma_500mer.prmtop pmma_500mer.inpcrd
Thank You
>
> On Mon, Jul 18, 2011 at 2:00 PM, David A Case <case.biomaps.rutgers.edu> wrote:
>> On Mon, Jul 18, 2011, KIRTANA S wrote:
>>>
>>> Thanks for the reply , I tried the minimzation again with serial run
>>> and sends me the same error .
>>> Now I checked my number of atoms and they are same .Though my initial
>>> mol2 file used was alright but when I used top2mol2 to
>>> convert the topology and coordinate files back to sybyl mol2 file ,
>>> the initial file is not proper . The same polymer chain for 200mer
>>> works good but this fails
>>
>> I'm pretty sure that top2mol2 was only intended for smallish molecules, and
>> might not work for a big system. But I don't understand why you are using
>> top2mol2 in the first place...it is not something that is ever in my personal
>> workflow. Without knowing anything at all about how you created the offending
>> coordinate file, it's hard to help in tracking down how it could be fixed.
>>
>> ....dac
>>
>>
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>
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Received on Fri Jul 22 2011 - 17:00:06 PDT
