On Nov 20, 2011, at 10:02 AM, FyD wrote:
> Dear Jason,
>
>> The "loadOFF" command in leap allows you to load any library files you have
>> laying around. The directories that are searched for the library files are
>> $AMBERHOME/dat/leap/lib as well as the current working directory. You can
>> add more directories to your search path via the -I flag to tleap. That is,
>>
>> tleap -I/path/to/my/libs
>
> ok thanks.
>
> We have developed a new force field library file format .
> q4md-forcefieldtools.org within LEaP.
>
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
> -I.3.4.- The mol3 file format
> http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
>
> regards, Francois
Francois,
I think this addition has the potential to simplify the use of tleap
and documentation for new residue development in the AMBER (and,
possibly, other) MD program.
However, one thing was not clear to me when I read the
-I.3.1- Features of the mol3 file format
section at
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php .
That writeup seems to imply that only the head atom can connect to
other atoms (not counting the tail atom). If I understand the writeup
correctly, this is an incomplete specification. I have had the need
in the past to have 4 connectX atoms. This involved leap forming bonds
between
residue N, connect2 and residue N+1, connect 2. Also between
residue N, connect3 and residue N+1, connect 3. These are in
addition to the normal
residue N-1, connect 1, and residue N, connect 0, and
residue N, connect 1, and residue N+1, connect 1 used to define
the polymer.
I can expand on that example either in personal email,
mldodson-at-comcast-dot-net, or in other ways, for example the
q4md-forcefieldtools forum, although I am not now a member of that
forum. I can give an explicit example in which this is the "natural"
way to handle two new residues (which have no useful or chemically
correct meaning except when taken as a pair.)
I would appreciate expansion to a broader specification to allow this
case. But maybe it is already there, and I misunderstood the
documentation.
Bud Dodson
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Sun Nov 20 2011 - 09:00:04 PST
