hi i tried to run the simulation with single alamethicin molecule but i am getting the same error as i was getting earlier. Warning: 1-4 interaction between 164 and>> 169 at distance 3.430 which is larger than the 1-4 table size 1.000 nm. I used the command $ genbox -cp alamethicin.gro -cs popc.gro -o system.gro my pdb file at 164 to 169 is: ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00 ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00 ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00 ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00 ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00 ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00. This is occuring at the start of equillibration step . I have not done any simulation as yet. I also tried pre-equillibrating the protein and directly simulating by restrain but that also is not working.
I cannot figure out the problem. Please help at Windows Live Ideas—so new they>>> haven’t>>>> even been officially released yet.>>>>>>>>>>>> http://www.msnspecials.in/windowslive/_______________________________________________>>>>>>> gmx-users mailing list gmx-users@gromacs.org>>>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users>> Please search the>>>>> archive at http://www.gromacs.org/search before posting!>> Please don't>>> post>> (un)subscribe requests to the list. Use the>> www interface or>> send>>> it to>> [EMAIL PROTECTED]>> Can't post? Read>>>>> http://www.gromacs.org/mailing_lists/users.php>>>>>>>>>>> =========================================================>> Justin A.>>>>> Lemkul> Graduate Research Assistant> Department of Biochemistry> Virginia>>>>>>> Tech> Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/>>>>>>> =========================================================>>>>>> _______________________________________________> gmx-users mailing list>>>>> gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users>>>>>>>> Please search the archive at http://www.gromacs.org/search before>> posting!>>>>>> Please don't post (un)subscribe requests to the list. Use the> www>>> interface>> or send it to [EMAIL PROTECTED]> Can't post?>> Read>>>>> http://www.gromacs.org/mailing_lists/users.php>>>>> _________________________________________________________________>> Call>>> friends with PC-to-PC calling -- FREE>>>>> http://get.live.com/messenger/overview>>>>>>> =========================================================>> Justin A.>>> Lemkul> Graduate Research Assistant> Department of Biochemistry> Virginia>>> Tech> Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/>>>>> =========================================================>>>> _______________________________________________> gmx-users mailing list>>> gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users>>>> Please search the archive at http://www.gromacs.org/search before posting!>>>> Please don't post (un)subscribe requests to the list. Use the> www>> interface>>> or send it to [EMAIL PROTECTED]> Can't post? Read>>> http://www.gromacs.org/mailing_lists/users.php>>> _________________________________________________________________>>> Windows Live Spaces is here! It’s easy to create your own personal Web>> site.>>> http://spaces.live.com/?mkt=en-in>>>>>>>> =========================================================>>>> Justin A. Lemkul>> Graduate Research Assistant>> Department of Biochemistry>> Virginia Tech>> Blacksburg, VA>> [EMAIL PROTECTED] | (540) 231-9080>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/>>>> =========================================================>>>> =========================================================>> Justin A. Lemkul> Graduate Research Assistant> Department of Biochemistry> Virginia Tech> Blacksburg, VA> [EMAIL PROTECTED] | (540) 231-9080> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/>> =========================================================> _______________________________________________> gmx-users mailing list gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/search before posting!> Please don't post (un)subscribe requests to the list. Use the> www interface or send it to [EMAIL PROTECTED]> Can't post? Read http://www.gromacs.org/mailing_lists/users.php _________________________________________________________________ Windows Live Spaces is here! It’s easy to create your own personal Web site. http://spaces.live.com/?mkt=en-in_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
