From owner-chemistry@ccl.net Mon Jun 28 09:14:01 2021 From: "Kjell Jorner kjell.jorner,+,gmail.com" To: CCL Subject: CCL: About the software to calculate Ring Puckering parameters Message-Id: <-54420-210628091240-5460-H/eBGTQl/fxXe3WUD4zPsg++server.ccl.net> X-Original-From: Kjell Jorner Content-Type: multipart/alternative; boundary="Apple-Mail=_A3E02338-4908-4298-9E0C-5238C7D8DFA2" Date: Mon, 28 Jun 2021 09:12:28 -0400 Mime-Version: 1.0 (Mac OS X Mail 14.0 \(3654.100.0.2.22\)) Sent to CCL by: Kjell Jorner [kjell.jorner{}gmail.com] --Apple-Mail=_A3E02338-4908-4298-9E0C-5238C7D8DFA2 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Cremer=E2=80=99s own Ring Puckering program used to be available from = this site: https://sites.smu.edu/dedman/catco/ring-puckering.html = =20 Instruction are still there, but the link to the code seems broken. I = would suggest reaching out to Elfi Kraka. Best, Kjell Jorner > 27 juni 2021 kl. 22:19 skrev Vlad Vassiliev vvv900[-]nci.org.au = : >=20 >=20 > Sent to CCL by: "Vlad Vassiliev" [vvv900~~nci.org.au] > Hi CCL Gurus, >=20 > Could you suggest me any software (binary or/and source code) to = calculate the Cremer-Pople Ring Puckering parameters for small cyclic = molecules (for example, for Tetrahydrofuran). >=20 > Thanks, > Vlad >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail=_A3E02338-4908-4298-9E0C-5238C7D8DFA2 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Cremer=E2=80=99s own Ring Puckering program used to be = available from this site: https://sites.smu.edu/dedman/catco/ring-puckering.html = ;
Instruction are still there, but the link to the code = seems broken. I would suggest reaching out to Elfi Kraka.

Best,
Kjell Jorner

27 juni 2021 kl. 22:19 skrev = Vlad Vassiliev vvv900[-]nci.org.au <owner-chemistry---ccl.net>:


Sent to CCL by: "Vlad  Vassiliev" [vvv900~~nci.org.au]
Hi = CCL Gurus,

Could you suggest me any = software (binary or/and source code) to calculate the Cremer-Pople Ring = Puckering parameters for small cyclic molecules (for example, for = Tetrahydrofuran).

Thanks,
Vlad



-=3D This is automatically added to each message by the = mailing script =3D-
To recover the email address of the = author of the message, please change
the strange = characters on the top line to the --- sign. You can also
look = up the X-Original-From: line in the mail header.

E-mail to subscribers: CHEMISTRY---ccl.net or use:
=      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST---ccl.net or use
=      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

=      http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/<= br class=3D"">
Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

If your mail bounces from CCL with 5.7.1 = error, check:
     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



= --Apple-Mail=_A3E02338-4908-4298-9E0C-5238C7D8DFA2-- From owner-chemistry@ccl.net Mon Jun 28 09:49:01 2021 From: "Daniel Roe daniel.r.roe-x-gmail.com" To: CCL Subject: CCL: About the software to calculate Ring Puckering parameters Message-Id: <-54421-210628092802-13545-Ymz8G3Q15w1PQGkqpXPbtA^_^server.ccl.net> X-Original-From: Daniel Roe Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Mon, 28 Jun 2021 09:27:43 -0400 MIME-Version: 1.0 Sent to CCL by: Daniel Roe [daniel.r.roe|a|gmail.com] Hi, You can use the 'pucker' command from the MD analysis program CPPTRAJ (available here: https://github.com/Amber-MD/cpptraj , or as part of AmberTools: https://ambermd.org/AmberTools.php ) to calculate ring puckering using either the method of Cremer & Pople or Altona & Sundaralingam. The input would look something like: parm trajin pucker p1 :1*C1’ :1*C2’ :1*C3’ :1*C4’ :1*O4’ cremer out pucker.dat run See the cpptraj manual (https://jenkins.jasonswails.com/job/amber-github/job/cpptraj/job/master/lastSuccessfulBuild/artifact/doc/CpptrajManual.pdf) for full details. Hope this helps, -Dan On Sun, Jun 27, 2021 at 11:39 PM Vlad Vassiliev vvv900[-]nci.org.au wrote: > > > Sent to CCL by: "Vlad Vassiliev" [vvv900~~nci.org.au] > Hi CCL Gurus, > > Could you suggest me any software (binary or/and source code) to calculate the Cremer-Pople Ring Puckering parameters for small cyclic molecules (for example, for Tetrahydrofuran). > > Thanks, > Vlad> > From owner-chemistry@ccl.net Mon Jun 28 11:45:01 2021 From: "Geoffrey Hutchison geoff.hutchison###gmail.com" To: CCL Subject: CCL: About the software to calculate Ring Puckering parameters Message-Id: <-54422-210628114419-3068-ndbYucavkZiIEopqY6LTlw*_*server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Type: multipart/alternative; boundary="Apple-Mail=_FBC4108E-2D7C-4D6E-A7B7-EE543DA26B57" Date: Mon, 28 Jun 2021 11:44:12 -0400 Mime-Version: 1.0 (Mac OS X Mail 14.0 \(3654.100.0.2.22\)) Sent to CCL by: Geoffrey Hutchison [geoff.hutchison!A!gmail.com] --Apple-Mail=_FBC4108E-2D7C-4D6E-A7B7-EE543DA26B57 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 > Cremer=E2=80=99s own Ring Puckering program used to be available from = this site: https://sites.smu.edu/dedman/catco/ring-puckering.html = =20 > Instruction are still there, but the link to the code seems broken. I = would suggest reaching out to Elfi Kraka. We published an article earlier this year analyzing ring puckering = motifs with Lucian Chan and Garrett Morris of Oxford = (https://doi.org/10.1021/acs.jcim.0c01144 = - Open Access)=09 The Python code is available on GitHub: https://github.com/lucianlschan/RING/ https://github.com/lucianlschan/RING/blob/master/Ring_Analysis.py Obviously, if it's useful in a paper, we'd appreciate a citation. :-) Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh:-:pitt.edu twitter: :-:ghutchis web: https://hutchison.chem.pitt.edu/= --Apple-Mail=_FBC4108E-2D7C-4D6E-A7B7-EE543DA26B57 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
Cremer=E2=80=99s own Ring Puckering = program used to be available from this site: https://sites.smu.edu/dedman/catco/ring-puckering.html = ;
Instruction are still there, but the link to the code = seems broken. I would suggest reaching out to Elfi = Kraka.

We = published an article earlier this year analyzing ring puckering motifs = with Lucian Chan and Garrett Morris of Oxford (https://doi.org/10.1021/acs.jcim.0c01144 - Open = Access) =

The Python code is available = on GitHub:

Obviously, if it's useful in = a paper, we'd appreciate a citation. :-)

Cheers,
-Geoff

---
Prof. Geoffrey = Hutchison
Department of Chemistry
University of = Pittsburgh
tel: (412) 648-0492
twitter: :-:ghutchis
= --Apple-Mail=_FBC4108E-2D7C-4D6E-A7B7-EE543DA26B57--