On 18/10/2010 10:31 PM, vinothkumar mohanakrishnan wrote:
Hi all
i added new atomtype for dichloroethane (DCE) and added the
corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp
respectively. given below are my additions to the corresponding files
respectively.
*ffoplsaa.rtp*
[ DCE ]
[ atoms ]
CLAA opls_967 -0.2270 1
CAB opls_966 0.2270 1
CAC opls_966 0.2270 2
CLAD opls_967 -0.2270 2
[ bonds ]
CLAA CAB
CAB CAC
CAC CLAD
[ angles ]
CLAA CAB CAC
CAB CAC CLAD
[ dihedrals ]
CLAA CAB CAC CLAD
*ffoplsaa.atp*
opls_966 14.02700 ; CH2 for DCE
opls_967 35.45300 ; CL for DCE
*ffoplsaabon.itp*
[bondtypes]
CLAA CAB 1 0.17870 194137.6 ; CL-CH2 for DCE
CAB CAC 1 0.15300 259408.0 ; CH2-CH2 for DCE
CAC CLAD 1 0.17870 194137.6 ; CL-CH2 for DCE
[angletypes]
CLAA CAB CAC 1 108.200 368.192 ; C-C-CL for DCE
CAB CAC CLAD 1 108.200 368.192 ; C-C-CL for DCE
[dihedraltypes]
CLAA CAB CAC CLAD 3 20.76096 -0.4184 27.011904
0.00000 0.00000 0.00000 ; for DCE
*ffoplsaanb.itp*
opls_966 CAB 6 14.02700 0.227 A 3.98000e-01
4.76976e-01 ; CH2 of DCE
opls_967 CLAA 17 35.45300 -0.227 A 3.16000e-01
0.20920e+01 ; Cl of DCE
*dce.pdb*
HETATM 1 CLAA DCE 1 6.300 -2.280 1.360 1.00
20.00 CL
HETATM 2 CAB DCE 1 5.060 -3.540 1.500 1.00
20.00 C
HETATM 3 CAC DCE 1 4.320 -3.740 0.170 1.00
20.00 C
HETATM 4 CLAD DCE 1 3.270 -2.350 -0.210 1.00
20.00 CL
After adding all this, when i run grompp i get the error as *fatal
error Unknown bond_atomtype CLAA*. can any one tell me why this happens?.
I can't tell until I know how you've invoked grompp, and how you
generated the .top file it needs, and which line of that .top grompp
doesn't like. When asking for help, please copy and paste all your
relevant commands, and any error messages in full, and any relevant
chunk of the .top. Check whether that .top file is #including the
correct .itp files.
Mark
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