Dear Tomas, Thanks for your information! I look at the website you mentioned: http://virtualchemistry.org/molecules/110-02-1/index.php The *top file is available and the atom opls-aa types are assigned on *top file.
But I can not find these parameters of dihedral angles from the default gmx (VERSION 4.5.5) directory of oplsaa.ff or the opls-aa (2005). For example: the parameters for dihedral of s-cw-cs-cs is missing Do you know where i can find these parameters? what versioni of opls-aa they are using? Thanks, Steven On Thu, Dec 6, 2012 at 9:08 AM, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. help about opls-aa for thiophene (Thomas Schlesier) > 2. How to merge Self-made ammonia .top with tip4p (Kenji Mochizuki) > 3. Re: Issue building template file for Gromacs 4.6-beta1 > (Roland Schulz) > 4. oplsff- need of gro and itp file -reg (venkatesh s) > 5. Re: oplsff- need of gro and itp file -reg (Justin Lemkul) > 6. Re: Parametrisation of the cyclic nucleotides in Gromos force > fields (Justin Lemkul) > 7. Re: Asymmetry in homo dimer simulation (Justin Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 6 Dec 2012 12:11:35 +0100 > From: Thomas Schlesier <[email protected]> > Subject: [gmx-users] help about opls-aa for thiophene > To: <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="ISO-8859-1"; format=flowed > > Have a look there: > http://virtualchemistry.org/molecules/110-02-1/index.php > > "virtualchemistry.org" is a really nice site (from David van der Spoel, > and others i think), which has many paramters for solvents for the GAFF > and OPLS force field. And also Physical properties for these. > > Greetings > Thomas > > > C4H4S. Thiophene is common compound . it seems oplss-aa does not have the > > parameters for it (such > > as dihedral angle). > > > > Any expert of opls-aa forcefield can help with ff parameters for > thiophene? > > Thanks very much! > > > > Steven > > > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
