Thanks, David. I will try it out and tell you how the results went. Best wishes, Art
--- David van der Spoel <[EMAIL PROTECTED]> wrote: > Arthur Roberts wrote: > > Hi, all, > > > > I have been trying to convert a small molecule > into > > oplsaa format using the x2top. The x2top doesn't > seem > > to recognize the connectivity specified in the n2t > > file. > > > > Below is the n2t file > > > > ; alkanes (first number is bond type and second > number > > is number of protons) > > C opls_138 4 H H H H ; alkane CH4 > > C opls_135 4 H H H * ; alkane CH3 > > C opls_136 4 H H C * ; alkane CH2 > > C opls_137 4 H C * * ; alkane CH > > C opls_139 4 C * * * ; alkane C > > H opls_140 1 C ; alkane H (sp3 > > hybridized > proton) > > ; alkenes (first number is bond type and second > number > > is number of protons) > > C opls_141 3 C C C ; alkene R2-C=R > > C opls_142 3 H C C ; alkene RH-C=R > > C opls_143 3 H H C ; alkene H2-C=R > > H opls_144 1 C ; alkene H-C= > > (sp2 hybridized > > proton) > > > > I made a top file of an aliphatic and all the > carbons > > were treated as if they were the first one. i.e. > > opls_138 > > > > Gromacs doesn't appear to recognize the > connectivity > > in ffgmx.n2t either. > > > > I would appreciate anyone's input. > > > > Best wishes, > > Art > > _______________________________________________ > > 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 > I presume this is in 3.3.1? > > try installing the CVS branch in a separate tree and > run x2top from > there. There have been a number of improvements in > that program. > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular > Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala > University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > 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 > _______________________________________________ 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
