[gmx-users] No default Proper Dih. types, U-B types and Bond types error???

[Mark Abraham]

On Wed, Mar 13, 2013 at 6:43 PM, 라지브간디 <rajiv at kaist.ac.kr> wrote:

> Dear all,
>
>
> I am doing MD simulation studies on hemoglobin heme ligated with CO. I
> used charmm27 and mentioned the all bond details such as bonds between CO,
> HIS with heme in specbond.dat. It does recognizes the bonds and created the
> bonds in topology file using pdb2gmx. Moreover, I have added the heme
> hydrogen details in aminoacids.hdb after searching few details in gromacs
> user page.
>
>
> However, i am struct with the steps in adding the ions to the protein as
> it gives the errors like
>
>
> No default Proper Dih. types ,
> No default U-B types
> No default Bond types
>
>
>
> I believe these faults are arise from the bonds which i mentioned in
> specbond.dat. I do have the parameter files of these heme-co ligand
> (literature and AMBER database) and do not know how do i interpret in here
> to avoid this problem?
>

grompp needs to be able to find parameters for all the interactions in your
system. Normally it can look them up from your forcefield files (go and
have a look at ffbonded.itp!) from the atom types. Here it complains that
it cannot do that. Either you need to copy and extend your force field
files with the parameter information you say you have so that grompp can do
the lookup, or you need to do the lookup for grompp and actually paste the
right fields into the topology where that bond/angle/dihedral is defined,
e.g.

[bond]
; i j functype b0 kb
1 2 1 0.33 23423

instead of

[bond]
; i j
1 2

The tables and info in chapter 5 of the manual are definitely your friends
here.

Mark


>
> Any suggestion and advice please.
>
>
> Thanks all.
>
>
> Raju
>
>
>
>
>
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