From owner-chemistry@ccl.net Wed Nov 2 08:18:01 2011 From: "werner schroedinger werner.schroedinger%a%googlemail.com" To: CCL Subject: CCL: Study folding and/or molecular dynamics of flexible part of a protein Message-Id: <-45808-111102070726-23302-fgaNHYM2UYdNWeiEK69HVQ:-:server.ccl.net> X-Original-From: werner schroedinger Content-Type: multipart/alternative; boundary=0015174489fc932a3904b0be796d Date: Wed, 2 Nov 2011 12:07:16 +0100 MIME-Version: 1.0 Sent to CCL by: werner schroedinger [werner.schroedinger#,#googlemail.com] --0015174489fc932a3904b0be796d Content-Type: text/plain; charset=ISO-8859-1 Thanks a lot Andy. Is MolSoft's software free to academics? On Tue, Nov 1, 2011 at 10:50 PM, Andrew Orry andy/amolsoft.com < owner-chemistry]_[ccl.net> wrote: > Werner > > You might find this new method helpful: > > Arnautova *et al* Development of a new physics-based internal coordinate > mechanics force field and its application to protein loop modeling. > Proteins. 2011 Feb;79(2):477-98http://www.ncbi.nlm.nih.gov/pubmed/21069716 > > Conformational sampling is carried out using the biased probability Monte > Carlo method in a new Internal Coordinate Mechanics force field. It is > incorporated into MolSoft's software http://www.molsoft.com/icm_pro.html. > > Thanks, > Andy > > -- > Andrew Orry Ph.D. > MolSoft LLC > Senior Research Scientist > 11199 Sorrento Valley Road, S209 > San Diego > CA 92121 > Tel: 858-625-2000 x108 > Fax: 828-625-2888www.molsoft.com > > > On 11/1/2011 8:33 AM, Werner Schroedinger werner.schroedinger*|* > googlemail.com wrote: > > Sent to CCL by: "Werner Schroedinger" [werner.schroedinger^-^googlemail.com > ] > In some PDB protein structure I would like to study flexibility in some concrete part of the molecule (small loop). I would like to perform > > a) protein folding where all the protein is rigid except the selected part, which remains totally flexible b) molecular dynamics, where it is only flexible the previously selected part > > Although this approach could seem unrealistic, I would like to know which method/programs, etc, would you recommend for performing this.E-mail to subscribers: CHEMISTRY]|[ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST]|[ccl.net or use**http://www.ccl.net/chemistry/sub_unsub.shtml > > > -- > Andrew Orry Ph.D. > MolSoft LLC > Senior Research Scientist > 11199 Sorrento Valley Road, S209 > San Diego > CA 92121 > Tel: 858-625-2000 x108 > Fax: 828-625-2888www.molsoft.com > > --0015174489fc932a3904b0be796d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks a lot Andy. Is MolSoft's software free to academics?


=
On Tue, Nov 1, 2011 at 10:50 PM, Andrew Orry and= y/amolsoft.com <owner-chemistry]_[ccl.net> wrote:
=20 =20 =20
Werner

You might find this new method helpful:

Arnautova et al Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins. 2011 Feb;79(2):477-98 http://www.ncbi.nlm.nih.gov/pubmed/21069716

Conformational sampling is carried out using the biased probability Monte Carlo method in a new Internal Coordinate Mechanics force field. It is incorporated into MolSoft's software http://www.molsoft.com/icm= _pro.html.

Thanks,
Andy
--=20
Andrew Orry Ph.D.
MolSoft LLC
Senior Research Scientist
11199 Sorrento Valley Road, S209
San Diego
CA 92121
Tel: 858-625-2000 x108
Fax: =
828-625-2888
www.molsoft.com

    

    On 11/1/2011 8:33 AM, Werner Schroedinger
    werner.schroedinger*|*googlemail.com wrote:
    

      
Sent to CCL by: "Werner  Schroedinger&quo=
t; [werner.schroedinger^-^googlemail.com
]
In some PDB protein structure I would like to study flexibility in some con=
crete part of the molecule (small loop). I would like to perform

a) protein folding where all the protein is rigid except the selected part,=
 which remains totally flexible b) molecular dynamics, where it is only fle=
xible the previously selected part

Although this approach could seem unrealistic, I would like to know which m=
ethod/programs, etc, would you recommend for performing this.E-mail to subs=
cribers: CHEMI=
STRY]|[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_messagehttp://www.c=
cl.net/chemistry/sub_unsub.shtml


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

Job: http://www.ccl.n=
et/jobs=20
Conferences: http://server.ccl.net/chemistry/announcements/co=
nferences/


Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

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



    

    

    

    
--=20
Andrew Orry Ph.D.
MolSoft LLC
Senior Research Scientist
11199 Sorrento Valley Road, S209
San Diego
CA 92121
Tel: 858-625-2000 x108
Fax: =
828-625-2888
www.molsoft.com

--0015174489fc932a3904b0be796d-- From owner-chemistry@ccl.net Wed Nov 2 08:53:00 2011 From: "Ramon Crehuet rcsqtc^^iqac.csic.es" To: CCL Subject: CCL:G: TDDFT question Message-Id: <-45809-111102084258-29378-yu44WBfbxtIDGY7A/XA3wA+/-server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 02 Nov 2011 13:46:26 +0100 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc() iqac.csic.es] Dear all, I do not know how to interpret some TDDFT results calculated with gaussian 09 and CAM-B3LYP functional. If I calculate triplet excited states from the ground state singlet, their energies are very close (in eV): 3.3, 3.4, 3.5, 3.5, 3.5, 3.6 If I calculate the lowest triplet state with CAM-B3LYP, it lies 4.2eV above the singlet. Is the error of 0.9eV normal? (this triplet corresponds to a pi-pi* excitation in a pyridine) If, from this triplet, I calculate with TDDFT more triplet excited states, I get the energies: 0.7, 1.2, 2.0, 2.3, 2.5, 2.7 So all the close-lying triplets found before are gone. My system contains 2 Au atoms coordinated to phosphines and pyridines (through a triple CC bond). I can tell you more structural details if you need them. I am thankful to any advice, Ramon