AMBER Archive (2003)

Subject: Re: AMBER: roar topology and coordinate files

From: M. L. Dodson (bdodson_at_scms.utmb.EDU)
Date: Mon Dec 29 2003 - 07:35:42 CST

On Monday 29 December 2003 03:11 am, PSR04996_at_mailstudenti.unimi.it wrote:
> Hi all,
> I use amber7 to perform molecular dynamic simulations with the sander
> module. I would like to do single point and minimization calculations
> on selected structures using an hybrid potential with the roar module.
> I was told that the files .top and .crd generated by xLeap or tLeap of
> amber7 are not read by roar. I would like to know if this problem holds
> even for .crd files generated by carnal and for .rst files whatever
> generated, and if a solution has been proposed for this problem
> (perhaps a minor modification in the source code whould be sufficient).
>
> Thank you in advance
>
> Stefano Pieraccini
>

Ah, its been a year since I messed with this, and I don't have the source or
the appropriate .crd and .top files here at home. As I recall, the problem
is a missing field in one of the first two lines of the coordinate file. I
am pretty sure I posted about the problem to the list about 14-15 months ago,
but I'm not sure I posted the workaround; I may have just sent that info to
D. Case and/or K. Merz (or not). If my memory is working correctly, a
restart file has the correct format. I suggest you do a very short sander
minimization and/or md run, then look at the beginning of the restart file
and compare it to the coordinate file generated by leap. There should be an
extra field in the restart file (in the second line, IIRC). If you find that
to be so, then just use the restart file as the coordinates for your roar
run. (Actually any restart file should suffice to just identify the missing
field, but not to determine its correct value). I think, but am not
completely sure, I determined the most appropriate solution was to generate a
restart file with a roar (not sander) MM (not hybrid MM/QM) run and use that.

If you really want to use the leap coordinates, I think you can just copy the
missing field to the leap file (but only if the parm files are the same for
the two types of coordinate files). Run some short tests to be sure
everything is OK. Looking at the roar source should clarify matters, but it
took me a while to find it, IIRC.

I don't know about carnal. Try it and see.

Suggestion to the AMBER maintainers:
A short perl or awk script to fix a leap coordinate file to be acceptable to
roar. I'll try to find some time to work on this if no one else does (but it
may be a while), so please let me know off list if you are going to work on
it. The rate limiting factor should be identifying the location in the roar
source where the appropriate line is read (in order to verify that the
problem can be easily fixed up in a post-leap step). IIRC, roar really does
need this information, so changing the roar source is not a viable solution.

Bud Dodson 

-- 
M. L. Dodson                                bdodson_at_scms.utmb.edu
409-772-2178                                FAX: 409-772-1790

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