Re: AMBER: Could not find cntrl namelist

From: Robert Duke <>
Date: Tue, 10 Jul 2007 17:57:54 -0400

Okay, I looked at this and saw no funny nonprinting special chars. What I
did see is a nonperiodic system (ntb = 0) with a PME simulation (igb = 0),
and no &ewald section. Now, pme does a periodic boundary condition by
default, but you can get a barebones vacuum simulation by specifying in an
&ewald namelist a value for eedmeth of 4 (bare coulomb) or 5
(distance-dependent dielectric). I sort of suspect, without looking at the
sander code, that there is a bug in input parsing that maybe is incorrectly
identifying this illegal combination of inputs, and producing the wrong
error message. This is a quick guess; I have not looked back at the sander
code (don't know which version anyway) and this is a nonissue with PMEMD
because I don't support non-generalized Born vacuum simulations at present.
I would first try sticking
after the &cntrl and see if that works. Sorry if I am off on this, but
thought a quick comment couldn't hurt much. These comments are based on
amber 9; probably true for 8 and 7 also.
Best Regards - Bob Duke

----- Original Message -----
From: "Francesco Pietra" <>
To: <>
Sent: Tuesday, July 10, 2007 5:11 PM
Subject: RE: AMBER: Could not find cntrl namelist

> 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
> --- 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 |
>> | Tel: +1 858 822 0854 | EMail:- |
>> | | PGP Key available on request |
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may
>> not
>> be read every day, and should not be used for urgent or sensitive issues.
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Received on Wed Jul 11 2007 - 06:07:53 PDT
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