Re: [AMBER] [Private q4md] R.E.D. Server: Private assistance

From: FyD <>
Date: Fri, 22 Aug 2014 21:27:23 +0200

Dear George,

> Apologes for the cross-posting; I also sent this email to the AMBER list

ups sorry I missed your email in the Amber mailing list; I copy/cut
the answer to the amber mailing list besides that private assistance...

> 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 message

I looked at P15600:
  -> it was deleted because I am too late...

> 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.
> I upload the archive with input files and the log rfom the RED job.

So I looked at the zip file you provided for the private assistance:
The System.config file looks ok; but the Project.config file has too
many stuffs in it that are not related to your molecule; it should not
be a problem but it looks like we have a small bug here; your best bet
is to start from a simple Project.config file:

MOLECULE1-TITLE = your-title

i.e. use only what you need...

regards, Francois

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Received on Fri Aug 22 2014 - 12:30:02 PDT
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