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 - 14:15:57 CST

On Monday 29 December 2003 07:35 am, M. L. Dodson wrote:
> 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

Sorry to follow up my own post. I found the following in my notebook:
<quote>
The format of a restart file for roar-cp MD is:
natoms time nlink
3 times natoms position coords + 3 times nlink link atoms coords

See file nhc_lib.F (restart file is unit 16). Search for
WRITE(16 this will give format.
</quote>

So it should suffice to just add the number of link atoms as a third field.
I'm guessing the format should be I5 in analogy with the format of
natoms, but you should check it yourself.

You can ignore all my speculations in my original reply.

Bud Dodson 

-- 
M. L. Dodson                                bdodson_at_scms.utmb.edu
409-772-2178                                FAX: 409-747-8608

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