From chemistry-request@ccl.net Sat Jul 18 15:41:01 1992
Date: 18-JUL-1992 13:46:06.37
From: WSONNEN@EAGLE.WESLEYAN.EDU
Subject: CHARMM DCD to DCD conversion
To: chemistry@ccl.net
Status: R

I posted a question over the new on how to take an existing CHARMm .DCD
file and create another .DCD file containing only selected atoms. 
I received some helpful suggestions from Themis Lazaridis and the
people at POLYGEN. 

Below is a CAHRMm script file which does what i want. It may not be
the best way but it works. After reading in a frame of a dynamics
into the main coordinate set, i delete selected atoms. This deletion
also deletes those atoms (bonds, etc) from the .PSF. Therefore, it
is necessary to reread the .PSF file before reading another frame
of the trajectory.

* Script file produced by WAYNE
* 
open write unit 7 Card name JUNK.LOG line
outu 7
bomlev -2
bann
 
OPEN READ UNIT 53 FILE NAME JUNK.PSF
READ PSF UNIT 53
OPEN READ UNIT 54 FILE NAME HE.DCD
OPEN WRIT UNIT 55 FILE NAME SMALL.DCD
TRAJ IWRITE 55 NFILE 3  
*

OPEN READ UNIT 51 CARD NAME HE.CRD
READ COOR CARD FREE UNIT 51 
CLOSE UNIT 51

OPEN WRIT UNIT 56 CARD NAME SMALL.CRD
WRITE COOR CARD UNIT 56 SELE BYNUM 1:542 END
*

SET 1 1
LABEL LOOP
   REWIND UNIT 53
   READ PSF UNIT 53
   REWIND UNIT 54
   READ COOR UNIT 54 FILE IFILE @1
   DELETE ATOM SELE BYNUM 543:2273 END
   TRAJ WRITE
   INCR 1 BY 1
   COOR INIT
   IF 1 LT 3.5 GOTO LOOP
STOP
 

From chemistry-request@ccl.net Sat Jul 18 02:06:10 1992
Date: Sat, 18 Jul 1992 13:11:55 +1000
From: apa@ccadfa.cc.adfa.oz.au (Alan P Arnold)
To: chemistry@ccl.net
Subject: ESP-charges from Mopac.
Status: R

Dear colleagues,

A couple of questions about Mopac6.0 that comes with Biosym's i
InsightII/ Discover nowadays...

     When you specify an ElectroStatic Potential calculation
     you get atom-centered point-charges on your molecule
     like those first suggested by Brent Besler et al (J.Comp.Chem.
     11, 431, 1990) which have been obtained by fitting the 
     semi-empirical ESP (AM1, MNDO etc) at points on a series
     of shells outside the (usually) Connolly surface.

     Question 1: Are the points on the C-surface the same ones you
     get if you request a 'surface point' picture in InsightII?

     If not, 
     Question 2: How does one visualise the Mopac ESP points with
     InsightII? (and color them according to the magnitude of the
     ESP)

     Question 3: What are likely consequences of disabling the few
     lines of Mopac which prevent the constrained-fitting of the ESP
     to the semi-empirical x,y,and z-components of the dipole moment 
     for charged molecules?

IMHO this type of charge is about as good as one can get for current
mechanics and dynamics calculations, but it would be *really nice*
to be able to update these charges every few steps to
take into account changes in ESP with changes in structure during
a simulation.  Because the ESP-fitting step is very time consuming, 
this seems a forlorn hope, but...

     a recent paper by Tasi, Kiricsi and Forster (J.Comp.Chem.
13, 371-9, 1992) shows how you can generate atom-centered point
charges by 'extended Mulliken population analysis' which are
in excellent agreement with those obtained by ESP-fitting - but
with 2-3 orders of magnitude less cpu time, so ...

     Question 4: Is anyone willing to incorporate this procedure
     into Mopac6. and save a lot of us, a lot of 'ESP' cpu time?

As always, thanks for listening.....
----
Alan Arnold             	     |  e-mail: apa@ccadfa.cc.adfa.oz.au
Chem. Department,University College  |  voice : +61 6 268 8080
Australian Defence Force Academy     |  fax   : +61 6 268 8002
CANBERRA  ACT 2600 Australia         |