AMBER Archive (2007)

Subject: RE: AMBER: Could not find cntrl namelist

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 10 2007 - 13:21:12 CDT

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

/\
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|\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 |

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