Jochen, Thank you!
Vitaly JH> I once built one from the standart opls-atoms. It is ENTIRELY UNTESTED! JH> I have absolutely no clue how good it is. In particular the partial JH> charges on the H and C may have to be improved. JH> best, Jochen JH> Here is also a pdb: JH> TITLE One Cyclohexane JH> REMARK THIS IS A SIMULATION BOX JH> CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1 JH> MODEL 1 JH> ATOM 1 CA CYC 1 26.075 25.752 1.621 1.00 0.00 JH> ATOM 2 HA1 CYC 1 26.881 25.711 0.887 1.00 0.00 JH> ATOM 3 HA2 CYC 1 25.289 25.092 1.251 1.00 0.00 JH> ATOM 4 CB CYC 1 25.534 27.188 1.727 1.00 0.00 JH> ATOM 5 HB1 CYC 1 25.141 27.510 0.762 1.00 0.00 JH> ATOM 6 HB2 CYC 1 26.351 27.869 1.969 1.00 0.00 JH> ATOM 7 CC CYC 1 24.440 27.294 2.801 1.00 0.00 JH> ATOM 8 HC1 CYC 1 23.568 26.715 2.493 1.00 0.00 JH> ATOM 9 HC2 CYC 1 24.106 28.329 2.891 1.00 0.00 JH> ATOM 10 CD CYC 1 24.941 26.784 4.162 1.00 0.00 JH> ATOM 11 HD1 CYC 1 24.135 26.825 4.896 1.00 0.00 JH> ATOM 12 HD2 CYC 1 25.727 27.444 4.533 1.00 0.00 JH> ATOM 13 CE CYC 1 25.482 25.349 4.056 1.00 0.00 JH> ATOM 14 HE1 CYC 1 24.665 24.668 3.814 1.00 0.00 JH> ATOM 15 HE2 CYC 1 25.875 25.027 5.021 1.00 0.00 JH> ATOM 16 CF CYC 1 26.577 25.242 2.982 1.00 0.00 JH> ATOM 17 HF1 CYC 1 27.448 25.821 3.290 1.00 0.00 JH> ATOM 18 HF2 CYC 1 26.911 24.208 2.892 1.00 0.00 JH> TER JH> ENDMDL JH> Here is the hdb entry. Add it to ffoplsaa.hdb: JH> CYC 6 JH> 2 4 HA CA CB CF JH> 2 4 HB CB CA CC JH> 2 4 HC CC CB CD JH> 2 4 HD CD CC CE JH> 2 4 HE CE CD CF JH> 2 4 HF CF CE CA JH> Here is the rtp entry. Add it to ffoplsaa.rtp and run pdb2gmx. JH> ; cyclohexane JH> [ CYC ] JH> [ atoms ] JH> CA opls_136 -0.120 1 JH> HA1 opls_140 0.060 1 JH> HA2 opls_140 0.060 1 JH> CB opls_136 -0.120 2 JH> HB1 opls_140 0.060 2 JH> HB2 opls_140 0.060 2 JH> CC opls_136 -0.120 3 JH> HC1 opls_140 0.060 3 JH> HC2 opls_140 0.060 3 JH> CD opls_136 -0.120 4 JH> HD1 opls_140 0.060 4 JH> HD2 opls_140 0.060 4 JH> CE opls_136 -0.120 5 JH> HE1 opls_140 0.060 5 JH> HE2 opls_140 0.060 5 JH> CF opls_136 -0.120 6 JH> HF1 opls_140 0.060 6 JH> HF2 opls_140 0.060 6 JH> [ bonds ] JH> CA HA1 JH> CA HA2 JH> CA CF JH> CA CB JH> CB HB1 JH> CB HB2 JH> CB CC JH> CC HC1 JH> CC HC2 JH> CC CD JH> CD HD1 JH> CD HD2 JH> CD CE JH> CE HE1 JH> CE HE2 JH> CE CF JH> CF HF1 JH> CF HF2 JH> Vitaly Chaban wrote: >> Guys, >> >> Does anybody have an already prepared topology of cyclohexane? >> >> Thanks. >> -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php