Subject: SUMMARY: From one molecule to another

From: [email-masked] (John R. Nash)
Date: Sat, 3 Feb 1996 22:29:39 -0600

My original post:

>        I am seeking a utility that will take as input the cartesian
>coordinates
>of compounds A and B and generate x number of intermediate structures in
>between the two by interpolation (i.e. morphing from one structure to the
>other). I know that some packages will do this sort of thing for "linear
>synchronous transit" calculations, but I need the input files for a
>computation where this is not included.  (The molecule is way too big for
>GAUSSIAN... could the program perhaps be convinced to calculate the
>coordinates w/o running the qm calculation on them?)  This seems like an
>simple enough utility to write, but my guess is that it must have been done
>by someone...

As I suspected, this is a problem tackled by many.  I've collected all of
the responses that have appeared on the list and in my mailbox together
here.  The method that I used was to use the -spline function of Babel,
since I was already familiar with the program.

----------------------------------------------------------------------
From: Pat Walters <[email-masked]>

Babel can do this.  Matt Stahl added some code to create a spline
between two structures.  If you contact Matt ([email-masked])
he can give you the details.

Pat
------------------------------------------------------------------
W. Patrick Walters, Ph.D.
Scientist, Computational Chemistry and Molecular Modeling
Vertex Pharmaceuticals, Inc., 40 Allston St., Cambridge, MA  02139
Voice: (617)576-3111   FAX: (617)576-2109
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From: Ernest Chamot <[email-masked]>

MOPAC, being a semiempirical method, can handle a much larger system than a
Gaussian ab initio calculation, and I thought that MOPAC would do the job
for you with a "SADDLE" calculation, selecting XYZ to keep the calculation
using cartesian coordinates, rather than internal coordinates.  I tried it
out, though, and the MOPAC Output file does indeed have the initial and
final geometries in cartesian coordinates, but the intermediate steps are
all in internal coordinate format!

You should be able to convert each of these internal coordinate Z-matrices
into a cartesian representation with an additional MOPAC run (1SCF) for each
step, but I'm afraid this isn't a very elegant solution.

EC
---
Ernest Chamot
Consultant in Computational Chemistry Applications
Chamot Laboratories, Inc.
530 E. Hillside Rd.
Naperville, Illinois 60540
(708) 637-1559 (Voice & Fax)
[email-masked]
----------------------------------------------------------------------

From: Wayne Huang <[email-masked]>

Seems you want to a dynamic constrain exercise. Coordinate driving which
allow one to generate a list of molecule by promoting its geometrical
parameters (can be more than one simultaneously or in sequence) of a
single structure, but this requires optimization of some sort, at least MM.

--Wayne

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|  Wayne Huang, Ph.D.           |  18401 Von Karman, Suite 370        |
|  Computational Chemist        |  Irvine, California 92715           |
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----------------------------------------------------------------------

From: [email-masked] (Willem Paul van Hoorn)

[author included source code for two programs. here are the headers]

#!/bin/ksh
#
# crd2mind_kollman : convert and append CHARMM .CRD file to an input for
BOSS MIND
# The Kollman reaction coordinate is generated: J.Chem.Phys. 97, 5108 (1992)
# lamda = 0: start structure; lambda = 1: final structure
# sigma/epsilon/atom symbol are not added
# Usage: crd2mind in[.CRD]
# by WPvH 1994
#

#!/bin/csh
#
# crd2mind_all_kolman : appends single MIND files to one,
# appends non bonded params
# lambda = 0: start structure; lambda = 1: final structure
# pastefile: paste -d" " lambda0.CRD lambda1.CRD > pastefile.paste
# by WPvH 1994

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Thanks to all who replied!!!

-john nash

-==-John R. Nash-==[email-masked]==-UW-Madison Chem. Dept-==-
                 --- "When in doubt, roll!" ---