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

[Ahmet yıldırım]

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



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