[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
>
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Ahmet Yıldırım
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