[gmx-users] No automatic terminus detection

[Mark Abraham]

On 9/12/2011 12:55 AM, Matthias Ernst wrote:
> Hi Mark,
>
> thanks for your reply.
>
> [...]
> > It knows that termini have to be different from mid-chain residues.
> [...]
>
> That answers my question, I think. I wanted to ask if it's possible to 
> just use whatever residue name is given without detection ofend- or 
> midchain residues.
> I guess you answer tells me that this is impossible, so I have to 
> change my system.
>
> That's not really what I expected (in fact, from a programmer's view, 
> I think it should be no problem to leave out terminus search) but 
> thanks for your help.

It will just use an .rtp entry if it matches, and later expect that all 
the atoms from the .rtp entry will be found.

Your coordinate file looks like it is missing some atoms (presumably so 
that valences are satisfied), and pdb2gmx doesn't know how to strip down 
.rtp entries into something sensible that matches your input. You either 
need to provide input that matches an .rtp entry, write a .tdb entry to 
modify things, or write a new .rtp entry.

Mark