Hi Chris, Thanks for your detailed message and it is very helpful. B.Nataraj
On Wed, 15 Nov 2006 22:01:32 -0500, [EMAIL PROTECTED] said: > you are correct that you must include the water as part of the same > molecule (as you appear to have already done for Zn). I assume that > protein_ion_A.itp contains only one [ moleculetypes ] section that has > the protein and also the zinc. Take a look at how Zn has been included > there. Repeat this procedure to include the water that you want to be > bonded. Then modify your coordinate file accordingly. You can get > water parameters from gromacs-3.3.1/share/gromacs/top/tip3p.itp (or > sub the name of your favourite water model). > > Note that this is intended as my best idea about how to go about doing > exactly what you have asked. I have no idea how this is going to > affect things like a temperature group that contains a protein, a > zinc, and a single water if you have multiple temperature coupling > groups. Also I am not sure if settle is going to work properly. > > There is no warranty associated with this next portion, I have never > tried it. I have included this just to be explicit about what I am > suggesting. Lets say you use tip4p and oplsaa: > > under [ atoms ] add: > 2901 opls_113 1 SOL OW 1 0.0 > 2902 opls_114 1 SOL HW1 1 0.52 > 2903 opls_114 1 SOL HW2 1 0.52 > 2904 opls_115 1 SOL MW 1 -1.04 > > under [ bonds ] add: > #ifdef FLEXIBLE > ; i j funct length force.c. > 2901 2902 2901 0.09572 502416.0 0.09572 502416.0 > 2901 2903 2901 0.09572 502416.0 0.09572 502416.0 > #endif > > under [ angles ] add: > #ifdef FLEXIBLE > ; i j k funct angle force.c. > 2902 2901 2903 1 104.52 628.02 104.52 628.02 > #else > [ settles ] > ; OW funct doh dhh > 2901 1 0.09572 0.15139 > #endif > > Then also add: > [ exclusions ] > 2901 2902 2903 2904 > 2902 2901 2903 2904 > 2903 2901 2902 2904 > 2904 2901 2902 2903 > > [ dummies3 ] > ; Dummy from funct a b > 2904 2901 2902 2903 1 0.128012065 > 0.128012065 > > > Then go back and add any bonds that you want between this water and > the protein or zinc. > > It is unclear to me if the [ exclusions ] section is necessary or even > advisable. > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
