[gmx-users] topology of cyclohexane

[Jochen Hub]

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
REMARK    THIS IS A SIMULATION BOX
CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1           1
MODEL        1
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
2        4 HA CA CB CF
2        4 HB CB CA CC
2        4 HC CC CB CD
2        4 HD CD CC CE
2        4 HE CE CD CF
2        4 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
************************************************