Thanks, Chris! I'm using AMBER FF, so those are the scaling factors in this force field. Actually I never used standard Gromacs/Gromos ff and always make my own top file from scratch.
Lianqing On Thu, 7 Dec 2006 [EMAIL PROTECTED] wrote: >> Thanks a lot, Janne! I finally got it! Thanks for your inspiration! I >> added 1-4 pairs in [pairs] and then got the right values. I thought >> Gromacs would automatically find 1-4 pairs. > >send the structure to pdb2gmx and the value of genpairs will be >determined from your ffXXX.itp file. As far as I know, this is only in >this way that the [pairs] section will be generated in the output.top >file. If your system is not a protein, then you need to add the paris >section (and in fact create the entire .top file) by hand. > >By the way, why are you using the combination of genpairs=yes >fudgeLJ=0.5 and fudgeQQ=0.8333 ? This is not a valid combination for >any force field that comes in the standard gromacs distribution. > >_______________________________________________ >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 > _______________________________________________ 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
