Re: [AMBER] Error in unit 9 inpcrd file

From: KIRTANA S <>
Date: Mon, 18 Jul 2011 14:44:46 -0400

 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 <> 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 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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Received on Fri Jul 22 2011 - 17:00:06 PDT
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