[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


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.

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.

Scanned by iCritical.

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