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
You shouldn't be using atom names in the [*types] directives. What you should
be using are the interpolated types from ffoplsaanb.itp, thus you have only
utilized opls_966 (CAB) and opls_967 (CLAA).
*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?.
Have you been sure to #include the correct (modified) force field files? That
is, if you made a local copy and adjusted them, these won't be the files that
pdb2gmx will #include by default.
-Justin
Regards
Vinoth
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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