Amber Archive Jun 2001: by subject

(no subject)
- bxiong (Fri Jun 22 2001 - 19:11:09 PDT)
2'-deoxy-uracil
- Anton B. Guliaev (Wed Jun 06 2001 - 15:36:01 PDT)
90 degree phase offset in AMBER?
- Kristin Lynne Meagher (Mon Jun 04 2001 - 10:14:27 PDT)
a correction, sorry
- Andreas Svrcek-Seiler (Fri Jun 08 2001 - 06:43:39 PDT)
Adding crystal water using tleap.
- Bill Ross (Sun Jun 03 2001 - 10:19:32 PDT)
- Sanjeev B.S. (Sun Jun 03 2001 - 08:04:51 PDT)
AMBER
- jim caldwell (Tue Jun 19 2001 - 15:30:17 PDT)
- Phil Cunningham (Tue Jun 19 2001 - 13:53:11 PDT)
Amber compiling on Alpha Clusters Redhat Linux
- Chuck Schneider (Thu Jun 28 2001 - 05:08:41 PDT)
AMBER on Hitachi SR8000
- Noriyuki Yamaotsu (Thu Jun 07 2001 - 19:19:09 PDT)
- Bill Ross (Thu Jun 07 2001 - 14:43:48 PDT)
- Florian Barth (Thu Jun 07 2001 - 13:22:32 PDT)
AMBER on mpi
- Marco Punta (Wed Jun 27 2001 - 10:39:46 PDT)
AMBER parameter database
- Dr Richard Bryce (Fri Jun 29 2001 - 09:47:18 PDT)
AmberFFC version 1.2
- Francois Dupradeau (Sun Jun 24 2001 - 13:49:29 PDT)
An Invitation From The Middle East Chemical Industry
- iec_at_emirates.net.ae (Sat Jun 16 2001 - 12:34:21 PDT)
Animating normal modes
- David Bevan (Mon Jun 11 2001 - 10:36:39 PDT)
atom coordinates
- Bill Ross (Mon Jun 11 2001 - 16:29:39 PDT)
- Troy Bothwell (Mon Jun 11 2001 - 15:47:59 PDT)
begginer's question about RESP and GAMESS
- Jones de Andrade (Tue Jun 26 2001 - 10:44:02 PDT)
begginer's question.
- jim caldwell (Tue Jun 26 2001 - 12:20:32 PDT)
benchmark on X-86
- Sanjeev B.S. (Tue Jun 05 2001 - 01:23:37 PDT)
Best Topolgy for Linux Cluster
- Sanjeev B.S. (Tue Jun 26 2001 - 05:17:51 PDT)
CARNAL
- Olga Carvalho (Thu Jun 21 2001 - 07:27:14 PDT)
CCl4 charge problem...
- Thomas.Fox_at_bc.boehringer-ingelheim.com (Wed Jun 27 2001 - 01:16:19 PDT)
- jim caldwell (Fri Jun 22 2001 - 14:03:13 PDT)
CCl4 charge problem... (part II)
- Thomas.Fox_at_bc.boehringer-ingelheim.com (Wed Jun 27 2001 - 03:04:17 PDT)
Charges for a 2-iodine-phenol
- stefania_at_mail.unimo.it (Mon Jun 25 2001 - 09:29:27 PDT)
compiling amber6 in linux clusters
- A.Madhumalar (Sun Jun 03 2001 - 09:35:16 PDT)
coordinate blowup in sander
- Carlos Simmerling (Fri Jun 15 2001 - 11:46:36 PDT)
- jim caldwell (Fri Jun 15 2001 - 10:54:53 PDT)
- Michael Cooney (Fri Jun 15 2001 - 09:29:05 PDT)
dsp3 hybrid for P ?
- Todd J. Minehardt (Sun Jun 03 2001 - 12:47:41 PDT)
Dual-processor performance.
- Sanjeev B.S. (Mon Jun 11 2001 - 23:45:24 PDT)
emin after molecular dynamics
- Nicole Silvester (Fri Jun 22 2001 - 00:41:06 PDT)
Energy calculation
- Prem Raj Joseph (Tue Jun 26 2001 - 09:34:38 PDT)
equilibrating water in sander
- Yong Duan (Wed Jun 20 2001 - 21:27:02 PDT)
- Elizabeth K. White (Wed Jun 20 2001 - 16:00:00 PDT)
Error in Gibbs
- Kian Kani (Tue Jun 05 2001 - 09:42:48 PDT)
error message.
- Andreas Svrcek-Seiler (Fri Jun 08 2001 - 04:36:41 PDT)
- Margaret Cheung (Fri Jun 08 2001 - 00:24:07 PDT)
error msg in leap
- schayg_at_puskin-a206.sote.hu (Wed Jun 06 2001 - 12:27:49 PDT)
- Eoin Galligan (Wed Jun 06 2001 - 10:30:43 PDT)
folding simulations
- David Case (Thu Jun 28 2001 - 17:27:00 PDT)
- Elizabeth K. White (Thu Jun 28 2001 - 14:52:19 PDT)
free energy method
- Eoin Galligan (Wed Jun 06 2001 - 02:34:53 PDT)
gb with explicit water molecules
- Guanglei Cui (Fri Jun 22 2001 - 09:05:52 PDT)
GFP chromophore force field parameters
- Dr Chris L. Brown (Wed Jun 13 2001 - 18:31:56 PDT)
gradual warming + partial solvation
- Eoin Galligan (Mon Jun 25 2001 - 07:59:44 PDT)
How is the random number used to generate random velocities?
- Andrew Hoofnagle (Mon Jun 11 2001 - 10:02:37 PDT)
How to minimization of Average structure?
- Bill Ross (Sun Jun 03 2001 - 11:24:15 PDT)
- Xiaolin Chuang (Sun Jun 03 2001 - 09:57:48 PDT)
ice cube flying through space
- Andreas Svrcek-Seiler (Sat Jun 02 2001 - 05:54:55 PDT)
- Marcela Madrid (Fri Jun 01 2001 - 08:10:53 PDT)
- Marcela Madrid (Fri Jun 01 2001 - 08:10:53 PDT)
igb=1 error message: Unable to find bonded partner for atom 239
- Guanglei Cui (Sat Jun 09 2001 - 13:46:03 PDT)
informations
- schayg_at_puskin-a206.sote.hu (Tue Jun 05 2001 - 08:39:03 PDT)
- Osvaldo A. Santos-Filho (Mon Jun 04 2001 - 13:31:11 PDT)
Is there a potential for speedup in the GB-code ?
- Andreas Svrcek-Seiler (Fri Jun 15 2001 - 08:05:36 PDT)
iwrap & TIP3P model water
- Jung-Hsing Lin (Fri Jun 22 2001 - 09:53:00 PDT)
- Xiaolin Chuang (Fri Jun 22 2001 - 09:20:06 PDT)
leap not reaing torsion from frcmod file
- Eoin Galligan (Thu Jun 07 2001 - 06:45:22 PDT)
LIE method
- Wei Wang (Wed Jun 06 2001 - 20:24:26 PDT)
- Katherine Wallis Abold (Wed Jun 06 2001 - 14:14:10 PDT)
Linux stability
- Stephane (Fri Jun 22 2001 - 15:05:29 PDT)
- Bill Ross (Fri Jun 22 2001 - 13:51:17 PDT)
Machine file for sgi
- kian kani (Mon Jun 25 2001 - 10:25:21 PDT)
make test.all
- Elizabeth K. White (Wed Jun 06 2001 - 14:22:46 PDT)
mm_pbsa
- samantha hughes (Thu Jun 14 2001 - 00:06:47 PDT)
My input problem in amber6 !
- A. Ababou (Mon Jun 25 2001 - 08:54:18 PDT)
Non-standard DNA bases
- David Konerding (Wed Jun 13 2001 - 07:41:09 PDT)
- Bill Ross (Tue Jun 12 2001 - 22:29:40 PDT)
- J Suggs (Tue Jun 12 2001 - 16:32:21 PDT)
- Bill Ross (Tue Jun 12 2001 - 14:39:05 PDT)
number of atoms for large system
- Shixiang Yan (Tue Jun 05 2001 - 12:36:50 PDT)
parallel sander
- Yuguang Mu (Thu Jun 21 2001 - 23:43:07 PDT)
- Sanjeev B.S. (Wed Jun 20 2001 - 10:39:23 PDT)
- Yuguang Mu (Wed Jun 20 2001 - 07:58:39 PDT)
Parameter for abasic nucleotide
- Numan Oezguen (Wed Jun 27 2001 - 19:48:58 PDT)
PDB old to new
- Jithesh P.V. (Tue Jun 26 2001 - 23:48:06 PDT)
PMF calculations
- Eoin Galligan (Tue Jun 19 2001 - 03:58:26 PDT)
Problem in MD!
- PRADIPTA Bandyopadhyay (Thu Jun 14 2001 - 10:16:59 PDT)
Problems with AMBER
- Bill Ross (Fri Jun 29 2001 - 16:23:06 PDT)
- John Finke (Fri Jun 29 2001 - 15:55:06 PDT)
- Bill Ross (Thu Jun 28 2001 - 19:49:52 PDT)
- Bill Ross (Thu Jun 28 2001 - 19:49:52 PDT)
- John Finke (Thu Jun 28 2001 - 18:04:52 PDT)
reflector limitations
- jim caldwell (Wed Jun 06 2001 - 07:51:05 PDT)
resp charges: ccl4 jag vs. g98
- jim caldwell (Wed Jun 27 2001 - 15:51:49 PDT)
Resp input confusion.
- jim caldwell (Tue Jun 26 2001 - 14:55:07 PDT)
RESP X GAMESS Dummie Question
- Jones de Andrade (Mon Jun 18 2001 - 10:22:11 PDT)
sander 6 warming up
- Andreas Svrcek-Seiler (Fri Jun 01 2001 - 06:53:35 PDT)
sander_classic no mdcrd
- Richard W Dixon (Fri Jun 01 2001 - 08:41:10 PDT)
- Richard W Dixon (Fri Jun 01 2001 - 08:41:10 PDT)
- Daniel Flint (Fri Jun 01 2001 - 07:06:10 PDT)
- Daniel Flint (Fri Jun 01 2001 - 07:06:10 PDT)
- Christoph Sotriffer (Fri Jun 01 2001 - 06:53:27 PDT)
summary of Zn+2 van der Waals radii responses
- Katherine Wallis Abold (Fri Jun 08 2001 - 07:43:03 PDT)
TIP3P
- Bill Ross (Thu Jun 28 2001 - 23:34:47 PDT)
- Guanglei Cui (Thu Jun 28 2001 - 22:22:57 PDT)
tleap input format
- A.Madhumalar (Wed Jun 27 2001 - 06:20:02 PDT)
torsion parameters needed
- Guanglei Cui (Thu Jun 28 2001 - 22:40:06 PDT)
water parameters+TIP3 water model
- jim caldwell (Tue Jun 19 2001 - 11:52:04 PDT)
- Satyavani Vemparala (Mon Jun 18 2001 - 13:00:00 PDT)
WHY NOT TRY IT?
- go5612gwe_at_arabia.com (Mon Jun 18 2001 - 12:02:17 PDT)
Wrong compilation artifacts on ES40s?
- Bill Ross (Sun Jun 24 2001 - 23:51:20 PDT)
- Sanjeev B.S. (Sun Jun 24 2001 - 13:17:48 PDT)
- Bill Ross (Sun Jun 24 2001 - 12:58:33 PDT)
- Sanjeev B.S. (Sun Jun 24 2001 - 11:43:11 PDT)
- Bill Ross (Sun Jun 24 2001 - 10:59:27 PDT)
zinc
- Nicoletta Pucello (Thu Jun 21 2001 - 01:39:03 PDT)
- pascal bonnet (Thu Jun 21 2001 - 01:11:24 PDT)
Zn+2 van der Waals radii
- Katherine Wallis Abold (Thu Jun 07 2001 - 15:16:14 PDT)

Amber Archive Jun 2001 by subject