[AMBER] tleap cannot handle dummies in the middle?

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Date: Fri, 11 Oct 2013 17:18:43 +0100

Hi,

I found a problem with leap handling dummy atoms when it is in the
middle of the atom sequence as in the attached example (test.mol2).
Looks like a bug to me.

For the hydrogen bonded to it pert is set to true and the bond between
the two recreated. Leap terminates with the following message.

!FATAL ERROR----------------------------------------
!FATAL: In file [unitio.c], line 1805
!FATAL: Message: 1-4: cannot add bond 7 8
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.
!
!ABORTING.

When the dummy is pushed to the end of the sequence as in test2.mol2
leap runs fine with the mol2 and the created parm file looks ok.

The attachment contains a leap script leap.in to built the output files.


Cheers,
Hannes.
-- 
Scanned by iCritical.



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Received on Fri Oct 11 2013 - 09:30:06 PDT
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