[AMBER] Problem with Firefly optimisation in R.E.D server

From: George Patargias <gpat.bioacademy.gr>
Date: Wed, 20 Aug 2014 12:06:44 +0300

Hello Francois,

We are trying to submit a RESP calculation job on the R.E.D server for a
small charged (-1) organic molecule.

According to the log file, the job (job id P15600) doesn't enter the
optimization stage. Before loading the PDB file, there is the following

Numero of atom of long pair is not integer
Extra point is not correct HA_INDEX

and at the end of the log file, the following message

Unknown type of circle with 5 or 6 atoms
Two different residue can not have two or more conect between each other

We have taken care of the atom type definitions in Project.config
according to AMBER libraries.

Any help would be greatly appreciated; thanks!


Dr. George Patargias
Postdoctoral Research Fellow
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27

Office: +302106597568

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Received on Wed Aug 20 2014 - 02:30:02 PDT
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