[AMBER] Ligand parameterization

From: Hira Jabeen <hira_bioinfo.yahoo.com>
Date: Tue, 3 Sep 2019 10:56:42 +0000 (UTC)

Hi everyone,
I am parameterizing a small ligand in Amber 18 with ambertools19.
On saving parameters, I get the following error:
> saveamberparm MEM MEM.prmtop MEM.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
!FATAL ERROR----------------------------------------
!FATAL:    In file [unitio.c], line 1810
!FATAL:    Message: 1-4: cannot add bond 4 5
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.
Ligand and leap files are attached.Need your advice.

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Received on Tue Sep 03 2019 - 04:00:02 PDT
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