AMBER Archive (2007)

Subject: Re: AMBER: Could not find cntrl namelist

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Jul 10 2007 - 21:21:07 CDT

Aha, last time I actually did this (a vacuum simulation) was with sander 6.
Checking through the various releases, automatically hammering eedmeth to 4
if ntb .eq. 0 and igb .eq. 0 was introduced in sander 7, 8, 9. We should
probably more clearly document this, as I couldn't recollect when I had done
it, but the amber 9 doc was consistent with my previous experience (guess
who mostly runs pmemd ;-)). Looks to me like the provided inputs are not
the ones that are producing the problem, as I successfully ran the
minimization on sander 7, 8, and 9 (and 6 won't work due to the "new" prmtop
format).
Best Regards - Bob

----- Original Message -----
From: "Robert Duke" <rduke_at_email.unc.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, July 10, 2007 5:57 PM
Subject: Re: AMBER: Could not find cntrl namelist

> 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
> &ewald
> eedmeth=4,
> /
> 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" <chiendarret_at_yahoo.com>
> To: <amber_at_scripps.edu>
> 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 <ross_at_rosswalker.co.uk> 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:- ross_at_rosswalker.co.uk |
>>> | http://www.rosswalker.co.uk | 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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>>
>>
>>
>>
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>
>
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