RE: AMBER: Could not find cntrl namelist

From: Francesco Pietra <>
Date: Tue, 10 Jul 2007 14:11:48 -0700 (PDT)

Hi Ross:
I'll study your suggestions below, which arrived when I had decided to simplify
the problem by running equatorial methylcyclohexane, prepared for xleap with
antechamber. The same issue "Could not find cntrl namelost" arose.

This time, contrary to all previous experience, I could quit the xleap window
without getting the "not saved" message. Contrary to my hope, it didn't
anticipate the solution.

I also run my eqeq molecule with different mdin, always getting the "Could not
..." error message.

Attached are all relevant files.


francesco pietra

--- Ross Walker <> wrote:

> Hi Francesco,
> > What I fear at this point is related to what I posted
> > yesterday about a remind
> > by David Case that antechamber treats single residues:
> The issue is that the only possible things that could be generating this
> error message is either there is something wrong with the mdin file, the
> incorrect file was specified with -i or there is some issue with read
> permissions of the mdin file. At this point in the code the prmtop file
> hasn't even been opened so it cannot be related to a problem with that.
> Could you please attach your mdin file to an email (as an actual attachment)
> direct from the copy on the machine on which you are having problems. If you
> have to ftp it to another machine to email it then make sure you select
> binary format for the transfer. Then we can take a look and see if there is
> something weird going on.
> Another option you could try as well is to create a brand new file on the
> machine on which you are running sander and explicitly type in, on that
> machine in vi, everything you want in the input file. That way you work
> around any kind of weird corruption and/or strange control characters that
> may have made it into the old file during the copying / cut / pasting etc.
> Seeing the exact input file as sander sees it on your machine will really
> help.
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
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Received on Wed Jul 11 2007 - 06:07:51 PDT
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