From owner-chemistry@ccl.net Tue Jul 22 06:08:01 2008 From: "sobia ahsan halim sobia_halim(0)yahoo.com" To: CCL Subject: CCL: Multiligand docking on AutoDock Tool Message-Id: <-37386-080722060636-32176-gZpXEmPpgqrQNFY3DBy5tQ^_^server.ccl.net> X-Original-From: "sobia ahsan halim" Date: Tue, 22 Jul 2008 06:06:32 -0400 Sent to CCL by: "sobia ahsan halim" [sobia_halim|,|yahoo.com] Hi All I am using autodock tool (adt) for the docking purpose and I am looking for any option of multi ligand docking on adt. Can any one please suggest me how to run multiple ligand file simultaneously???? or is there any script available to perform virtual screening??? Kindly let me know...Thanks a lot in advance. Bye. From owner-chemistry@ccl.net Tue Jul 22 07:16:00 2008 From: "Raj s r.subramanian-*-ipc.uni-stuttgart.de" To: CCL Subject: CCL: restarting freq. calculations. Message-Id: <-37387-080722071430-14107-Gs02Pu6aVkGz2IDVRHJkRg(~)server.ccl.net> X-Original-From: "Raj s" Date: Tue, 22 Jul 2008 07:14:26 -0400 Sent to CCL by: "Raj s" [r.subramanian/./ipc.uni-stuttgart.de] Dear CCL members, i have a problem in restarting freq. calculations.. my route section is as below:- %Mem=1500mw %NProc=4 #GFInput b3lyp/gen NoSymm pseudo=read scf=(maxcycles=1000) freq=Numer /...molecule coordinated in Z-matrix /...basis sets, etc **** after 3 days the job got aborted (due to less calculation time).. Now i want to restart from checkpoint file...so i copied the chk point file in to the location where i have my original input file...then i changed the route to:- %Mem=1500mw %NProc=4 #GFInput b3lyp/gen NoSymm pseudo=read scf=(maxcycles=1000) freq=Numer,restart /*here i dint include anything...just the above 3 lines and keyword restart...*/ after changing the route i resubmitted the job like this:- gauss_sub inputfilename checkpointfilename but i always get some errors... kindly suggest me what can i do and how to restart.. i also made a backup of all files including the checkpoint files.. thanks and regards, raj From owner-chemistry@ccl.net Tue Jul 22 09:56:01 2008 From: "Ol Ga eurisco1 ~~ pochta.ru" To: CCL Subject: CCL:G: restarting freq. calculations. Message-Id: <-37388-080722093346-30694-/COChbspKCb8gIdBYLCb2Q_._server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 22 Jul 2008 09:33:42 -0400 Sent to CCL by: "Ol Ga" [eurisco1]*[pochta.ru] Dear Raj s! An error are In Your route section. Plese, see the correct route below (I think it works :-)): %chk=chk_name # GFInput b3lyp/gen NoSymm pseudo=read scf=(maxcycles=1000) # freq=(Numer,restart) I cite a point from Gaussian 03 manual Restart This option restarts a numerical frequency calculation after the last completed geometry (analytic frequency calculations are not restartable). A failed numerical frequency job may be restarted from its checkpoint file by simply repeating the route section of the original job, adding the Restart option to the Freq keyword. No other input is required. Sincerely, Ol Ga From owner-chemistry@ccl.net Tue Jul 22 10:42:00 2008 From: "Tristan Youngs t.youngs|-|qub.ac.uk" To: CCL Subject: CCL: Aten's traditional follow-up. Message-Id: <-37389-080722103625-14291-3LXKy+swEPI/4NpqR8+LFQ__server.ccl.net> X-Original-From: "Tristan Youngs" Date: Tue, 22 Jul 2008 10:36:20 -0400 Sent to CCL by: "Tristan Youngs" [t.youngs_-_qub.ac.uk] Once more, esteemed scientists, It has just been brought to my attention that the version of Aten released yesterday has a hideous bug in it that means all coordinate data is written out incorrectly. Damn my shoddy programming! This has been fixed, and new versions (still 0.99.2) will appear on the website within the next few hours. If anybody used it and lost their favourite coordinates file, please accept my apologies! Back to the doghouse... Tris. From owner-chemistry@ccl.net Tue Jul 22 22:21:01 2008 From: "Ping Lin plin1112(a)gmail.com" To: CCL Subject: CCL: error in VASP polarization calculation using Berry phase Message-Id: <-37390-080722170219-14718-qBz0ys9oMKOkHPBYessrUg a server.ccl.net> X-Original-From: "Ping Lin" Date: Tue, 22 Jul 2008 17:02:14 -0400 Sent to CCL by: "Ping Lin" [plin1112^gmail.com] Dear all, We try to use vasp to calculate polarization using berry phase as suggested in the manual. During the berry phase calculation, it always stops with an error in the OUTCAR: Error in subroutine BERRY: did not find all determinants Matrix CMK is not an nxn matrix for ISTR = 1 j = 0 Can anyone tell us how to carry out the calculation, even for the example in vasp manual (NaF)? Thank you in advance. From owner-chemistry@ccl.net Tue Jul 22 22:56:00 2008 From: "TaeBum Lee tzl0002-.-auburn.edu" To: CCL Subject: CCL: NEIGHBOR keyword in CRYSTAL06 Message-Id: <-37391-080722224145-19992-B9IqUzRrEs1IkdhyOR9K/A!^!server.ccl.net> X-Original-From: "TaeBum Lee" Date: Tue, 22 Jul 2008 22:41:41 -0400 Sent to CCL by: "TaeBum Lee" [tzl0002-$-auburn.edu] Hi, Does anyone has full example file to generate molecular fragment that contains the four H-Bonds using NEIGHBOR keyword in CRYSTAL03/06? I would like to extract first neighbor shell (most nearest molecular fragments for one arbitary molecule) of molecular cluster from crystal structure. In CRYSTAL06 manual, there is only a comment that NEIGHBOR needs complete CRYSTAL input. I couldn't understand the exact meaning of "complete" CRYSTAL input. Regards, TaeBum From owner-chemistry@ccl.net Tue Jul 22 23:30:00 2008 From: "neeraj misra neerajmisra * hotmail.com" To: CCL Subject: CCL: optimization Message-Id: <-37392-080722225311-24626-J3jW+9AAre+vlJo1hdDM9w=server.ccl.net> X-Original-From: "neeraj misra" Date: Tue, 22 Jul 2008 22:53:08 -0400 Sent to CCL by: "neeraj misra" [neerajmisra_+_hotmail.com] The following is the input file of an optimization calculation of a trimer of aluminium and antimony.It is showing an error of inexpensive integrals.What can be changed in the input. # B3LYP/LanL2DZ opt(VTight) IOP(6/7=3) trimer of Al-Sb 0 2 Al 0.000000 0.000000 0.000000 Sb 0.000000 0.000000 3.145800 Sb 3.067523 0.000000 4.230333