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
