>(1) I downloaded equilibrated methanol box (pdb) with opls from the gromacs website >(I need an all-atom model for MeOH). When I pdb2gmx, I get the following error message:
Why are you running it rhough pdb2gmx? Is there a .itp or .top file in the zip file you downloaded? If so, then that is what you use. You don't run it through pdb2gmx, that is from taking a pdb file for proteins and generating the topology files. >(2) What I really want is an all-atom butanol/water or methanol/water (1:3 in mole fraction) mixture >with about 400 molecules total. How do people usually generate initial coordinate file for such a system? Doesn't really matter too much, you can start with a very regular crystal like packing, you can use the genconf script to do that, you randomise it (but there isn't a script with GROMACS that does that very well currently, will have to run your own or use someone else's). >(3) Does opls/tip4p sound like a reasonable combination for the simulation of the methanol/water system? >If not, could you please recommend one? Best idea is to check the literature on that one, what has been done perviously along the lines of what you are looking to do. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9073 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
