[gmx-users] topology of cyclohexane

[Vitaly Chaban]

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: chaban at univer.kharkov.ua
skype: vvchaban
tel.: +38-097-8259698