From owner-chemistry@ccl.net Mon Jun 27 11:43:01 2016 From: "Wadud Miah wadud.miah(a)nag.co.uk" To: CCL Subject: CCL: Fortran Modernisation Workshop - Southampton and STFC Message-Id: <-52252-160627113555-21552-cPDPqZxY+54nqg71fYePbw%%server.ccl.net> X-Original-From: "Wadud Miah" Date: Mon, 27 Jun 2016 11:35:54 -0400 Sent to CCL by: "Wadud Miah" [wadud.miah,,nag.co.uk] Free Fortran Modernisation Workshop in the UK This two day computational science-centric practical hands on workshop is aimed at Fortran programmers who want to write modern and efficient code, or modernise existing codes, to make it more readable and maintainable by encouraging good software engineering practices. The workshop will cover tools and libraries that are commonly used in computational science and engineering. Click on the link below for further details and registration: Free for all: 27-28/OCT Daresbury - https://eventbooking.stfc.ac.uk/news-events/fortran-modernisation-workshop Free for academics only: 28-29/JUL Southampton - http://www.nag.co.uk/soton-07-2016 I can be reached at wadud.miah^nag.co.uk for further information. From owner-chemistry@ccl.net Mon Jun 27 13:31:01 2016 From: "Kshatresh Dutta Dubey kshatresh * gmail.com" To: CCL Subject: CCL: Amber+ chemshell help Message-Id: <-52253-160627132848-1874-OBdXmB13bhJUGl9xg6q2Gw|,|server.ccl.net> X-Original-From: Kshatresh Dutta Dubey Content-Type: multipart/alternative; boundary=001a11401e2a056a45053645dac2 Date: Mon, 27 Jun 2016 20:28:41 +0300 MIME-Version: 1.0 Sent to CCL by: Kshatresh Dutta Dubey [kshatresh*o*gmail.com] --001a11401e2a056a45053645dac2 Content-Type: text/plain; charset=UTF-8 Dear Users, I wonder if someone can help me to run a QM/MM calculation using Amber in chemshell program. I am using Amber + turbomole (though it is not QM program specific, I tried with Orca and getting same problem) for a QM/MM project. The QM/MM runs fine if I there is no scission of any chemical bond, eg. I am putting water or substrate in QM region. However when there is scission of a chemical bond, chemshell stops working after printing following in output file: group charges and members - calculation turbomole 1 : 0.00000 ** QM group ** : 2289 2 : 0.00000 ** QM group ** : 2290 3 : 0.00000 ** QM group ** : 2291 4 : 0.00000 ** QM group ** : 2292 5 : 0.00000 ** QM group ** : 2293 6 : 0.00000 ** QM group ** : 2294 7 : 0.00000 ** QM group ** : 2295 qm - mm group distances (cutoff is 99.000000) 1 (QM region) 2 (QM region) 3 (QM region) 4 (QM region) 5 (QM region) 6 (QM region) 7 (QM region) Computing charge shift boundary corrections ..and then it aborts. I will be very much thankful if someone can suggest me to figure out the problem. -- With best regards ************************************************************************************************ Kshatresh Dutta Dubey Post Doctoral Researcher, Lise Meitner Center for Computational Quantum Chemistry Hebrew University of Jerusalem Israel Jerusalem, Israel --001a11401e2a056a45053645dac2 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Users,

I wonder if someone can hel= p me to run a QM/MM calculation using Amber in chemshell program.=C2=A0

I am using Amber + tu= rbomole (though it is not QM program specific, I tried with Orca and gettin= g same problem) for a QM/MM project. The QM/MM runs fine if I there is no s= cission of any chemical bond, eg. I am putting water or substrate in QM reg= ion. However when there is scission of a chemical bond, chemshell stops wor= king after printing following in output file:=C2=A0
=C2=A0
group charges and members -= calculation turbomole
=C2=A0 =C2=A0 1 : =C2=A0 0.00000 ** =C2=A0= QM group =C2=A0 ** : 2289
=C2=A0 =C2=A0 2 : =C2=A0 0.00000 ** =C2= =A0QM group =C2=A0 ** : 2290
=C2=A0 =C2=A0 3 : =C2=A0 0.00000 ** = =C2=A0QM group =C2=A0 ** : 2291
=C2=A0 =C2=A0 4 : =C2=A0 0.00000 = ** =C2=A0QM group =C2=A0 ** : 2292
=C2=A0 =C2=A0 5 : =C2=A0 0.000= 00 ** =C2=A0QM group =C2=A0 ** : 2293
=C2=A0 =C2=A0 6 : =C2=A0 0.= 00000 ** =C2=A0QM group =C2=A0 ** : 2294
=C2=A0 =C2=A0 7 : =C2=A0= 0.00000 ** =C2=A0QM group =C2=A0 ** : 2295
qm - mm group distanc= es (cutoff is 99.000000)
=C2=A0 =C2=A0 1 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0(QM region)
=C2=A0 =C2=A0 2 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0(QM region)
=C2=A0 =C2=A0 3 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0(QM region)
=C2=A0 =C2=A0 4 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0(QM region)
=C2=A0 =C2=A0 5 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= (QM region)
=C2=A0 =C2=A0 6 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(QM= region)
=C2=A0 =C2=A0 7 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(QM re= gion)
Computing charge shift boundary corrections

..and then it aborts.=C2=A0
I will be very much t= hankful if someone can suggest me to figure out the problem.=C2=A0

--
With best regar= ds
**************************************************************= **********************************
Kshatresh Dutta Dubey
Post = Doctoral Researcher,
Lise Meitner Center for Computational Qu= antum Chemistry
Hebrew University of Jerusalem Israel
Jeru= salem, Israel


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