[gmx-users] Proline on OPLSSaa

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 11 09:16:16 CET 2008


Hi Mauro,

The .top says it all: you haven't specified parameters. Just listing
the bonds, angles and dihedrals in the .rtp file is not enough. You'll
have to assign parameters to them. Check the entries (notably PRO and
ACE) in the .rtp file of your choice...

Cheers,

Tsjerk

On Feb 11, 2008 12:02 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623



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