From owner-chemistry@ccl.net Wed Sep 15 10:51:01 2021 From: "Eric Henon eric.henon : univ-reims.fr" To: CCL Subject: CCL:G: calculation of mechanical stress on molecule Message-Id: <-54455-210915095019-25132-trTzqxnur9ig1Yk49K+GFw:+:server.ccl.net> X-Original-From: Eric Henon Content-Type: multipart/alternative; boundary="00000000000012c29205cc08fa8c" Date: Wed, 15 Sep 2021 15:50:00 +0200 MIME-Version: 1.0 Sent to CCL by: Eric Henon [eric.henon- -univ-reims.fr] --00000000000012c29205cc08fa8c Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Aretemi, I don't know exactly what you expect, but I think to the code Flexible developed by Marie Brut in Toulouse, it requires the oordinates and Hessian matrix as input (compatible with AMBER, Gromacs, Gaussian, ... outputs), and it allows for computing the so-called static modes describing the deformation induced by external forces. https://homepages.laas.fr/mbrut/drupal/node/36 [2009] M. Brut, A. Este=CC=80ve, G. Landa, G. Renvez, M. Djafari Rouhani. T= he Static Modes: An alternative approach for the treatment of macro and bio-molecular induced-fit flexibility. Eur. Phys. J. E 28, 17 (2009) Hope this will help. Eric Le mar. 14 sept. 2021 =C3=A0 17:18, Artemi Bendandi artemi.bendandi|-|gmail= .com < owner-chemistry---ccl.net> a =C3=A9crit : > > Sent to CCL by: "Artemi Bendandi" [artemi.bendandi!A!gmail.com] > Hi everyone! > > I'm writing to ask for suggestions on software with which to calculate > mechanical stress on > atoms/residues on snapshots of an MD trajectory (.pdb files). I found CAM= S > and mdStress but they don't > seem to be maintained/documented/used(?). > > I was wondering if anyone had any suggestions. Bear in mind that we need > something that works on > nucleic acids as well as protein. > > Thanks in advance! > > Cheers, > Artemi Bendandi > > Postdoctoral Fellow > PhD, Physics Computational Biophysicist > Istituto Italiano di Tecnologia (IIT) > Genoa, Italy > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --00000000000012c29205cc08fa8c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Aretemi,

I don't know exactly = what you expect, but I think to the code Flexible
developed=C2=A0= by Marie Brut in Toulouse, it requires the oordinates
and Hessian= matrix as input (compatible with AMBER, Gromacs, Gaussian, ... outputs),
and it allows for computing the so-called static modes
d= escribing the deformation induced by external forces.=C2=A0

<= /div>
[2009] M. Brut, A. Este=CC=80ve, G. La= nda, G. Renvez, M. Djafari Rouhani. The Static Modes: An alternative approach for the treatment of macro and bio-molecular induced-fit flexibili= ty. Eur. Phys. = J. E 28, 17 (2009)

Hope this will help.

Eric

=C2=A0


Le=C2=A0mar. 14 sept. 2021 =C3=A0=C2=A017:18, Artemi Bendan= di artemi.bendandi|-|gmail.com <owner-chemistry---ccl.net> a =C3= =A9crit=C2=A0:
<= br> Sent to CCL by: "Artemi=C2=A0 Bendandi" [artemi.bendandi!A!gmail.com]<= br> Hi everyone!

I'm writing to ask for suggestions on software with which to calculate = mechanical stress on
atoms/residues on snapshots of an MD trajectory (.pdb files). I found CAMS = and mdStress but they don't
seem to be maintained/documented/used(?).

I was wondering if anyone had any suggestions. Bear in mind that we need so= mething that works on
nucleic acids as well as protein.

Thanks in advance!

Cheers,
Artemi Bendandi

Postdoctoral Fellow
PhD, Physics=C2=A0 Computational Biophysicist
Istituto Italiano di Tecnologia (IIT)
Genoa, Italy



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY---ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST---ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

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

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/


--00000000000012c29205cc08fa8c--