[gmx-users] endcapping

[Anton Feenstra]

w.j.schravendijk at students.pharm.uu.nl wrote:
> 
> I edited the pdb to include the terminal N into the last residue (instead
> of being a residue of its own) and it worked, using -nosort and -ter as
> options to pdb2gmx. -nosort was necessary, while gromacs would have forced
> a carboxyl end to it otherwise.

I'm not so sure about that, actually, since -nosort would not keep
the atom order in your .gro and your .top file the same, while this
is an absolute requirement by grompp (you will get atom name mismatch
warnings if this is so when you run grompp). '-ter' should already
cause pdb2gmx to ask you the type of terminus to use, where you
should choose the appropriate ones for both N and C termini.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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