[gmx-users] unknown cmap torsion between atoms

[Steven Neumann]

On Fri, May 25, 2012 at 4:18 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 25/05/2012 7:52 PM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> My system is made of 3 proteins. As I want to use distance restraints
>> dynamics between atoms belonging to each of them I have to produce topoloy
>> with one moleculetype. I used pdb2gmx -chainsep interactive (I used merge:
>> yes).
>>
>> Then when I process to grompp the error: "unknown cmap torsion between
>> atoms  ......."
>>
>> These atoms belong to the last residue of the chain A and to the first
>> residue of Chain B. How to get rid of this? Please, help.
>>
>
> What version is this? I seem to recall fixing this bug at some stage.
>
> Mark
>

Its 4.5.4 - but the atoms belonging to these residues of one chain are
created on my own. I added them to residuetypes.dat and to my
aminoacids.rtp. They are nonbonded group of residues forming a planar
surface. When I remove their CMAP the same error occurs between next two
proteins which are formed of existing bonded residues. Do you have an idea
how to deal with this?

Steven


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