Re: [gmx-users] topology of cyclohexane
I once built one from the standart opls-atoms. It is ENTIRELY UNTESTED! I have absolutely no clue how good it is. In particular the partial charges on the H and C may have to be improved. best, Jochen Here is also a pdb: TITLE One Cyclohexane REMARKTHIS IS A SIMULATION BOX CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 CA CYC 1 26.075 25.752 1.621 1.00 0.00 ATOM 2 HA1 CYC 1 26.881 25.711 0.887 1.00 0.00 ATOM 3 HA2 CYC 1 25.289 25.092 1.251 1.00 0.00 ATOM 4 CB CYC 1 25.534 27.188 1.727 1.00 0.00 ATOM 5 HB1 CYC 1 25.141 27.510 0.762 1.00 0.00 ATOM 6 HB2 CYC 1 26.351 27.869 1.969 1.00 0.00 ATOM 7 CC CYC 1 24.440 27.294 2.801 1.00 0.00 ATOM 8 HC1 CYC 1 23.568 26.715 2.493 1.00 0.00 ATOM 9 HC2 CYC 1 24.106 28.329 2.891 1.00 0.00 ATOM 10 CD CYC 1 24.941 26.784 4.162 1.00 0.00 ATOM 11 HD1 CYC 1 24.135 26.825 4.896 1.00 0.00 ATOM 12 HD2 CYC 1 25.727 27.444 4.533 1.00 0.00 ATOM 13 CE CYC 1 25.482 25.349 4.056 1.00 0.00 ATOM 14 HE1 CYC 1 24.665 24.668 3.814 1.00 0.00 ATOM 15 HE2 CYC 1 25.875 25.027 5.021 1.00 0.00 ATOM 16 CF CYC 1 26.577 25.242 2.982 1.00 0.00 ATOM 17 HF1 CYC 1 27.448 25.821 3.290 1.00 0.00 ATOM 18 HF2 CYC 1 26.911 24.208 2.892 1.00 0.00 TER ENDMDL Here is the hdb entry. Add it to ffoplsaa.hdb: CYC 6 24 HA CA CB CF 24 HB CB CA CC 24 HC CC CB CD 24 HD CD CC CE 24 HE CE CD CF 24 HF CF CE CA Here is the rtp entry. Add it to ffoplsaa.rtp and run pdb2gmx. ; cyclohexane [ CYC ] [ atoms ] CA opls_136 -0.120 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 CB opls_136 -0.120 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CC opls_136 -0.120 3 HC1 opls_140 0.060 3 HC2 opls_140 0.060 3 CD opls_136 -0.120 4 HD1 opls_140 0.060 4 HD2 opls_140 0.060 4 CE opls_136 -0.120 5 HE1 opls_140 0.060 5 HE2 opls_140 0.060 5 CF opls_136 -0.120 6 HF1 opls_140 0.060 6 HF2 opls_140 0.060 6 [ bonds ] CA HA1 CA HA2 CA CF CA CB CB HB1 CB HB2 CB CC CC HC1 CC HC2 CC CD CD HD1 CD HD2 CD CE CE HE1 CE HE2 CE CF CF HF1 CF HF2 Vitaly Chaban wrote: Guys, Does anybody have an already prepared topology of cyclohexane? Thanks. -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-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
Re[2]: [gmx-users] topology of cyclohexane
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 REMARKTHIS IS A SIMULATION BOX JH CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1 JH MODEL1 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 24 HA CA CB CF JH 24 HB CB CA CC JH 24 HC CC CB CD JH 24 HD CD CC CE JH 24 HE CE CD CF JH 24 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 listgmx-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
[gmx-users] topology of cyclohexane
Guys, Does anybody have an already prepared topology of cyclohexane? Thanks. -- Vitaly ___ gmx-users mailing listgmx-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
