Re: [AMBER] tleap error

From: Akinpelu Olayinka <>
Date: Fri, 8 Nov 2019 11:50:09 +0000 (UTC)

 From the error message, the problem is with the bond between atoms 2245 and 2246. Kindly check them out.


Ola. On Friday, November 8, 2019, 01:31:38 PM GMT+2, MYRIAN TORRES RICO <> wrote:

I have a problem with tleap, this error appears:
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
!FATAL ERROR----------------------------------------
!FATAL:    In file [unitio.c], line 1783
!FATAL:    Message: 1-4: cannot add bond 2245 2246
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.

I have looking for about this error and it seems that a problem with 
the connects in my ligand in the pdb, but I have compared two pdb 
corresponding at the same molecule (ligand and complex), and I haven't 
find differents. I have attached both pdb for you to help me.
The "ptn3rig.pdb" doesn't give problems, and "ptn8rig.pdb" yes...

What can I do to resolve this problem? I have proved a lot of changes 
and nothing work it...

Thanks in advance,


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Received on Fri Nov 08 2019 - 04:00:03 PST
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