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

[Ahmet yıldırım]

Hi,

There are two H1D residue in modified pdb file and one H1E residue. ZN atom
in H1E are bound to OW and ND1 atoms in H1E and NE2 atom in H1D. That is,
Zinc has four bond.

              NE2(H1D)
                 ı
(H1E)ND1-ZN-OW(H1E)
                 ı
              NE2(H1D)

specbond.dat:
Line 1:H1E    ND1    1       H1E      ZN      1       0.2   H1E    H1E
Line 2:H1E    OW     1       H1E      ZN      1       0.2   H1E    H1E
Line 3:H1D    NE2    1       H1E       ZN      1       0.2   H1D    H1E

After pdb2gmx:
Linking H1D-94 NE2-754 and H1E-119 ZN-920...
Linking H1D-96 NE2-775 and H1E-119 ZN-920...
Linking H1E-119 ND1-952 and H1E-119 ZN-920...
Linking H1E-119 OW-921 and H1E-119 ZN-920..

I know the above linkings are correct.

I wonder, should I change as the following the line 3 in specbond.dat
because there are two H1D residue in structure?
H1D    NE2     1     H1E        ZN       2       0.2   H1D   H1E




2014-04-06 11:48 GMT+03:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:

> Hi Ahmet,
>
> Nothing wrong with specbond at this point. The bonds are correctly added,
> and apparently the bondtypes are read correctly too, because grompp only
> starts complaining at the point of angles. Check the atomtypes
> corresponding to the atoms involved in those angles in the .itp file that
> is generated.
>
> By the way, the message from moderator is due to the constant replying in
> the thread, including the previous mails. It's getting pretty lengthy like
> that. Sometimes it's good to keep only the parts of earlier messages that
> are directly being replied too.
>
> Cheers,
>
> Tsjerk
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-- 
Ahmet Yıldırım