[gmx-users] A problem of adding new bond parameters

[Mark Abraham]

On Sun, Mar 24, 2013 at 6:42 AM, spin <spin at mail.ustc.edu.cn> wrote:

> Hello, everyone,
>     I have tried to create a mutant of CYS, the CYC, which the S was
> replaced with a C at the end of its side chain. After using pdb2gmx to
> build
> the .top file, I added bond and nonbond parameters to link the side chain
> of
> two CYC as the disulfide bond for CYS. Also all necessary force field
> parameters have been added, especially those in ffbonded.itp and
> ffnonbond.itp. But when I use grompp, it give the following information:
>   /ERROR 1 [file TP-2.top, line 421]:
>   No default Bond types/
>

There's a contradiction somewhere. If "necessary parameters have been
added" then grompp would not find something to complain about on line 421.
What's there? Are your #includes referring to the forcefield files you
think they are?

Mark


>   There are 45 errors like this. The atom types of the side chain of CYC
> are
> described by GCenFF and those of the main chain are described by CHARMM.
> There are bond types, angle types and dihedral types of atoms from both the
> main side and the side chain. I created them just by replace the CHARMM
> atom
> types with GCenFF atom types of the side chain. For example, the angle type
> *HB   CT2   CT1* was replaced with *HGA2         CG321   CT1*.
>   Later I found that there were angle types and dihedral types in .top file
> missed in ffbonded.itp for both CYS and CYC. The topology of CYS can be
> recognized normally by grompp, while the one of CYC can not. Can someone
> tell me the reason?
>
> Thank you!
>
> Qing Liu
>
>
>
> --
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