[gmx-users] Proline on OPLSSaa
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Feb 11 00:02:37 CET 2008
Mauro Puppett wrote:
>
> Hi all,
> I'm trying to run a simulation of a proline in water tip5p with OPLSaa ff.
<snip>
> and it works fine till i run grompp which says:
>
> ERROR 0 [file "proline.top", line 182]:
> No default Ryckaert-Bell. types
> ERROR 0 [file "proline.top", line 191]:
> No default Ryckaert-Bell. types
> ERROR 0 [file "proline.top", line 193]:
> No default Ryckaert-Bell. types
> ERROR 0 [file "proline.top", line 201]:
> No default Ryckaert-Bell. types
Well, what's on these lines? Probably you're mis-naming some atom types,
but you'll need to do your own leg-work finding out which ones!
Mark
> This is my .top file:
>
> ; This is your topology file
> ; %E
> ;
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
>
> ; Include water topology
> #include "tip5p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
>
> [ moleculetype ]
> ; Name nrexcl
> Protein 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> 1 opls_239 1 APR N 1 -0.776797 14.0067 ; qtot -0.7768
> 2 opls_246 1 APR CA 2 -0.158578 12.011 ; qtot -0.9354
> 3 opls_058 1 APR C1 3 0.95425 12.011 ; qtot 0.01887
> 4 opls_062 1 APR OS1 4 -0.71999 15.9994 ; qtot -0.7011
> 5 opls_235 1 APR C2 5 0.808979 12.011 ; qtot 0.1079
> 6 opls_059 1 APR OS 6 -0.616492 15.9994 ; qtot -0.5086
> 7 opls_245 1 APR CD 7 -0.150278 12.011 ; qtot -0.6589
> 8 opls_136 1 APR CB 8 -0.404838 12.011 ; qtot -1.064
> 9 opls_140 1 APR HB1 9 0.24345 1.008 ; qtot -0.8203
> 10 opls_136 1 APR CG 10 -0.450709 12.011 ; qtot -1.271
> 11 opls_140 1 APR HB2 11 0.226125 1.008 ; qtot -1.045
> 12 opls_140 1 APR HG1 12 0.223126 1.008 ; qtot -0.8218
> 13 opls_140 1 APR HG2 13 0.242534 1.008 ; qtot -0.5792
> 14 opls_140 1 APR HD1 14 0.23943 1.008 ; qtot -0.3398
> 15 opls_140 1 APR HD2 15 0.239331 1.008 ; qtot -0.1005
> 16 opls_140 1 APR HA 16 0.262623 1.008 ; qtot 0.1622
> 17 opls_468 1 APR CE 17 -0.252649 12.011 ; qtot -0.09048
> 18 opls_469 1 APR HE1 18 0.216104 1.008 ; qtot 0.1256
> 19 opls_469 1 APR HE2 19 0.214466 1.008 ; qtot 0.3401
> 20 opls_469 1 APR HE3 20 0.212312 1.008 ; qtot 0.5524
> 21 opls_236 1 APR OB 21 -0.606932 15.9994 ; qtot -0.05453
> 22 opls_135 1 APR CF 22 -0.687405 12.011 ; qtot -0.7419
> 23 opls_140 1 APR HF1 23 0.262125 1.008 ; qtot -0.4798
> 24 opls_140 1 APR HF2 24 0.224449 1.008 ; qtot -0.2554
> 25 opls_140 1 APR HF3 25 0.255303 1.008 ; qtot -6.101e-05
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 5 1
> 1 7 1
> 2 3 1
> 2 8 1
> 3 4 1
> 3 6 1
> 4 17 1
> 5 21 1
> 5 22 1
> 7 10 1
> 7 14 1
> 7 15 1
> 8 9 1
> 8 10 1
> 8 11 1
> 10 12 1
> 10 13 1
> 17 18 1
> 17 20 1
> 22 23 1
> 22 24 1
> 22 25 1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 4 1
> 1 6 1
> 1 9 1
> 1 11 1
> 1 12 1
> 1 13 1
> 1 23 1
> 1 24 1
> 1 25 1
> 2 12 1
> 2 13 1
> 2 14 1
> 2 15 1
> 2 17 1
> 2 21 1
> 2 22 1
> 3 5 1
> 3 7 1
> 3 9 1
> 3 10 1
> 3 11 1
> 3 18 1
> 3 20 1
> 4 8 1
> 5 8 1
> 5 10 1
> 5 14 1
> 5 15 1
> 6 8 1
> 6 17 1
> 7 9 1
> 7 11 1
> 7 21 1
> 7 22 1
> 8 14 1
> 8 15 1
> 9 12 1
> 9 13 1
> 11 12 1
> 11 13 1
> 12 14 1
> 12 15 1
> 13 14 1
> 13 15 1
> 21 23 1
> 21 24 1
> 21 25 1
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 2 1 5 1
> 2 1 7 1
> 5 1 7 1
> 1 2 3 1
> 1 2 8 1
> 3 2 8 1
> 2 3 4 1
> 2 3 6 1
> 4 3 6 1
> 3 4 17 1
> 1 5 21 1
> 1 5 22 1
> 21 5 22 1
> 1 7 10 1
> 1 7 14 1
> 1 7 15 1
> 10 7 14 1
> 10 7 15 1
> 14 7 15 1
> 2 8 9 1
> 2 8 10 1
> 2 8 11 1
> 9 8 10 1
> 9 8 11 1
> 10 8 11 1
> 7 10 8 1
> 7 10 12 1
> 7 10 13 1
> 8 10 12 1
> 8 10 13 1
> 12 10 13 1
> 4 17 18 1
> 4 17 20 1
> 18 17 20 1
> 5 22 23 1
> 5 22 24 1
> 5 22 25 1
> 23 22 24 1
> 23 22 25 1
> 24 22 25 1
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2 c3 c4 c5
> 5 1 2 3 3
> 5 1 2 8 3
> 7 1 2 3 3
> 7 1 2 8 3
> 2 1 5 21 3
> 2 1 5 22 3
> 7 1 5 21 3
> 7 1 5 22 3
> 2 1 7 10 3
> 2 1 7 14 3
> 2 1 7 15 3
> 5 1 7 10 3
> 5 1 7 14 3
> 5 1 7 15 3
> 1 2 3 4 3
> 1 2 3 6 3
> 8 2 3 4 3
> 8 2 3 6 3
> 1 2 8 9 3
> 1 2 8 10 3
> 1 2 8 11 3
> 3 2 8 9 3
> 3 2 8 10 3
> 3 2 8 11 3
> 2 3 4 17 3
> 6 3 4 17 3
> 3 4 17 18 3
> 3 4 17 20 3
> 1 5 22 23 3
> 1 5 22 24 3
> 1 5 22 25 3
> 21 5 22 23 3
> 21 5 22 24 3
> 21 5 22 25 3
> 1 7 10 8 3
> 1 7 10 12 3
> 1 7 10 13 3
> 14 7 10 8 3
> 14 7 10 12 3
> 14 7 10 13 3
> 15 7 10 8 3
> 15 7 10 12 3
> 15 7 10 13 3
> 2 8 10 7 3
> 2 8 10 12 3
> 2 8 10 13 3
> 9 8 10 7 3
> 9 8 10 12 3
> 9 8 10 13 3
> 11 8 10 7 3
> 11 8 10 12 3
> 11 8 10 13 3
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> %E in water
>
> [ molecules ]
> ; Compound #mols
> Protein 1
> SOL 2390
>
> Can somebody pelase tell what I'm doing wrong?
> Thanks in advance
> Mauro Puppett
>
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