[gmx-users] Re: One molculetype for 3 proteins

[Tsjerk Wassenaar]

Hi Steven,

There will be three dihedrals spanning a break. Make sure to remove all of
them. Of course pdb2gmx shouldn't just connect the chain ends... Maybe you
can file it as a bug.

Cheers,

Tsjerk

On May 25, 2012 3:11 PM, "Steven Neumann" <s.neumann08 at gmail.com> wrote:

Yes, it works (-chainsep interactive: merge = yes ) but when you process to
grompp there is an error:

Unknown cmap torsion between atoms 6002 6004 6006 6017 6021

pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A with
first three residues of chain B. Removing these lines does not solve the
problem. Any suggestions appreciated!



On Fri, May 25, 2012 at 9:57 AM, Steven Neumann <s.neumann08 at gmail.com>wrote:

>
>
> > On Thu, May 24, 2012 at 10:04 PM, Francesca <
> francesca.stanzione at unina.it> wrote: >> >> I checked ...
>
> Yes, it works (-chainsep interactive: merge = no ) but when you process to
> grompp there is an error:
>
> Unknown cmap torsion between atoms 6002 6004 6006 6017 6021
>
> pdb2gmx takes the cmap for the atoms e.g. last two residues of chain A
> with first three residues of chain B. Does removing this lines will be
> reasonable or some torsions wont be taken into account?
>
> Steven
>
> >> >> >> -- >> View this message in context:
> http://gromacs.5086.n6.nabble.com/One-molculetype-for-3...
>
>

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