Re: AMBER: Could not find cntrl namelist

From: M. L. Dodson <>
Date: Tue, 10 Jul 2007 17:25:17 -0500

Francesco Pietra wrote:
> 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.
> Thanks
> francesco pietra

This input file runs fine for me. I think your sander compilation
must be bogus somehow. I'm using sander compiled with g95.

Bud Dodson

PS, where did you get the mdinfo file? I got one that differs
only in the number of steps, 272 vs. 274 (and everything else on
the NSTEP data line, but differs only in the last few decimal

> --- 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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M. L. Dodson
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Received on Wed Jul 11 2007 - 06:07:53 PDT
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