[gmx-users] part2-adding metal-bonding parameters to a force field

Ahmet yıldırım ahmedo047 at gmail.com
Sat Apr 5 21:57:54 CEST 2014


Hi,

I did 0.205 length between Zn and OZ in specpond.dat and ffbonded.itp.
There is Zn-OZ bond anymore. But there is still 9 error after grommp.

After pdb2gmx command:
..
Linking HIS-94 NE2-754 and ZWA-262 ZN-2081...
Linking HIS-96 NE2-775 and ZWA-262 ZN-2081...
Linking HIS-119 ND1-952 and ZWA-262 ZN-2081...
Linking ZWA-262 ZN-2081 and ZWA-262 OZ-2082...
...


2014-04-05 20:09 GMT+03:00 Ahmet yıldırım <ahmedo047 at gmail.com>:

> Sorry, I get "Message body is too big: 52376 bytes with a limit of 50 KB"
> from list moderator.
>
> I did as you said. I created the ZWA complex in pdb.
> pdb file:
> ...
> ATOM   2080  O   LYS A 261     -24.090 -10.437  34.386  1.00
> 35.64           O1-
> ATOM   2081  ZN  ZWA A 262      -6.760  -2.012  15.320  1.00
> 5.29           ZN
> ATOM   2082  OZ  ZWA A 262      -5.555  -0.748  16.011  1.00
> 8.54           O
> TER    2083      ZWA A 262
> ...
>
> After pdb2gmx command:
> ...
> Linking HIS-94 NE2-754 and ZWA-262 ZN-2081...
> Linking HIS-96 NE2-775 and ZWA-262 ZN-2081...
> Linking HIS-119 ND1-952 and ZWA-262 ZN-2081...
>
> Opening force field file
> /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
>  Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
> Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
> Checking for duplicate atoms....
> ...
>
> But I get the following errors after grommp. grompp doesnt still throw
> errors. I think there is something weird about specbond.dat and
> ffbonded.itp?
>
> After grompp command:
> ERROR 1 [file protein.top, line 21983]:
>   No default Angle types
>
> ERROR 2 [file protein.top, line 21984]:
>   No default Angle types
>
> ERROR 3 [file protein.top, line 22053]:
>   No default Angle types
>
> ERROR 4 [file protein.top, line 22054]:
>   No default Angle types
>
> ERROR 5 [file protein.top, line 22685]:
>   No default Angle types
>
> ERROR 6 [file protein.top, line 22687]:
>   No default Angle types
>
> ERROR 7 [file protein.top, line 26853]:
>   No default Angle types
>
> ERROR 8 [file protein.top, line 26854]:
>   No default Angle types
>
> ERROR 9 [file protein.top, line 26856]:
>   No default Angle types
>
> specbond.dat:
> 11
> ..
> HIS     ND1     1       ZWA     Zn      1       0.205   HIDZ    ZNW
> ;modified
> HIS     NE2     1       ZWA     Zn      1       0.205   HIEZ    ZNW
> ;modified
> ZWA     Zn      1       ZWA     OZ      1       0.23    ZNW     ZOH2
> ;modified
>
> residuetypes.dat:
> ..
> ZNW    protein ;modified
> ZOH2    protein ;modified
> HIDZ    Protein ;modified
> HIEZ    Protein ;modified
> ZWA     protein ;modified
>
> aminoacids.hdb:
> ZWA    1 ;modified
> 2    7    HZ    OZ
> ZNW    1 ;modified
> 2    7    HZ    OZ
> ZOH2    1 ;modified
> 2    7    HZ    OZ
> ..
>
> aminoacids.rtp:
> [ ZNW ];modified
>  [ atoms ]
>     ZN   ZN            0.89230   0
>     OZ   OZ           -0.8824    0
>    HZ1   HZ            0.5001    0
>    HZ2   HZ            0.5001    0
>  [ bonds ]
>     ZN   OZ
>     OZ   HZ1
>     OZ   HZ2
>
> [ ZOH2 ];modified
>  [ atoms ]
>     ZN   ZN            0.89230   0
>     OZ   OZ           -0.8824    0
>    HZ1   HZ            0.5001    0
>    HZ2   HZ            0.5001    0
>  [ bonds ]
>     OZ   HZ1
>     OZ   HZ2
> [ ZWA ];modified
>  [ atoms ]
>     ZN   ZN            0.89230   1
>     OZ   OZ           -0.8824    2
>    HZ1   HZ            0.5001    3
>    HZ2   HZ            0.5001    4
>  [ bonds ]
>     ZN   OZ
>     OZ   HZ1
>     OZ   HZ2
>
> atomtypes.atp:
> ..
> OZ                16.00000    ; modified
> HZ                 1.00800    ; modified
> ZN                65.40000      ; modified
>
> ffnonbonded.itp:
> OW           8      16.00    0.0000  A   1.76820e-01  6.371092e-01
> ;modified
> OZ           8      16.00    0.0000  A   3.15061e-01  6.36386e-01
> ;modified
> HZ           1       1.008   0.0000  A   0.00000e+00  0.00000e+00
> ;modified
> Zn          30      65.4     0.0000  A   1.10000e-01  5.23250e-02 ;modified
> ZN          30      65.4     0.0000  A   1.10000e-01  5.23250e-02 ;modified
>
> ffbonded.itp:
> [ bondtypes ]
> ..
>   ZN NA         1    0.20500   16744.0 ;modified
>   ZN NB         1    0.20500   16744.0 ;modified
>   ZN OZ         1    0.23000   16744.0 ;modified
>   OZ HZ         1    0.10120   221682.2 ;modified
> [ angletypes ]
> ..
> CR  NA  ZN           1   126.0       83.720 ;modified
> CW  NB  ZN           1   126.0       83.720 ;modified
> NA  ZN  NB           1   109.5       96.278 ;modified
> NB  ZN  NB           1   109.5       96.278 ;modified
> NA  ZN  OZ           1   109.5       96.278 ;modified
> NB  ZN  OZ           1   109.5       96.278 ;modified
> ZN  OZ  HZ           1   124.0       83.720 ;modified
> HZ  OZ  HZ           1   104.5     4186.000 ;modified
> [ dihedraltypes ]
> ..
>  X   ZN  NA  X     9       0.0      0.00000     3  ;modified
>  X   ZN  NB  X     9       0.0      0.00000     3  ;modified
>  X   ZN  OZ  X     9       0.0      0.00000     3  ;modified
>
>
>
> --
> Ahmet Yıldırım
>



-- 
Ahmet Yıldırım


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