Hi Justin, I wanted to use the only tip3p but I do not have the tip3p.gro file but only the tip3p.tip file. I also have the tip4p.gro and tip5p.gro file. Can I also use them?
> > > On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi Justin, >> >> yes I removed all the old resulting files and did everything again. So >> now >> there is the topology and coordinate file with only NA and CL and not >> NA+ >> or CL-. >> I also checked whether the molecules are listed in the same order as in >> the .gro file and it is the case. So that is also correct. >> >> What do you mean with: >> >>> What does your [molecules] directive specify? >> >> My [molecules] part in the topology file looks like this: >> >> [ molecules ] >> ; Compound #mols >> Protein_chain_A 1 >> DUM 20088 >> SOL 13428 >> NA 29 >> CL 29 >> > > I see no reason this would not work. However, I just noticed from your > previous > message: > >>>> ; Include water topology >>>> #include "amber03.ff/tip3p.itp" >>>> >>>> >>>> >>>> ; Include topology for ions >>>> #include "amber03.ff/ions.itp" >>>> >>>> #include "amber03.ff/spc.itp" >>>> #include "amber03.ff/dum.itp" >>>> > > You're using two different water models, so things are getting overridden > there. > With AMBER03, you should be using TIP3P, not SPC. The conflicting water > models suggest you've made manual modifications to the topology. Perhaps > there > is some error as a result. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
