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
-- 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" [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: 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.ccl.net/chemistry/sub_unsub.shtmlBefore posting, check wait time at: http://www.ccl.net Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
-- 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