[gmx-users] endcapping

[Anton Feenstra]

w.j.schravendijk at students.pharm.uu.nl wrote:
> 
> Dear Gromacs users,
> 
> I would like to test an endcapped 26 residue-peptide. The carboxyl
> end-group is amidated: C(O)NH2 instead of C(O)OH.
> 
> In the pdb file, the amide group is mentioned as an extra residue and
> looks something like this:
> 
> HETATM  201  N   NH2 A  27      13.279   5.297  18.956  1.00 48.71
> TER     202      NH2 A  27
> 
> pdb2gmx gives the error: no alpha carbon present in residue 27.

Can't find that error message in the source code. 
Which version of GROMACS are you using?

> How should I proceed? I guess there are several options:
> - create an extra NH2 entry in the n-termini database ffgmx.tdb
> - create an extra residue in the residue database, resembling my
> end-capped residue.
> - remove the NH2 residue from the pdb file and try to put it back after
> pdb2gmx by editing the .top and .gro file. However, how do I check if the
> edited topology and coordinate file are correct?

That last option is dangerous, since you need to keep track of all
bonds, angles, dihedrals and improper dihedrals beging defined
correctly. That also relates to you remark of knowing whether your
edited top is correct...

By the way, there actually *is* a terminus type 'NH2' already
in the -n.tdb. I've used that myself and it seems to work fine.
However, then you should not have the atom as a separate residue,
but part of the preceding residue (both residue number and name 
should be identical). That should work. Ofcourse you need to run
'pdb2gmx -ter' to select the proper terminus type. 

But also the approach you have taken should work, since there 
also *is* a 'NH2' residue entry in the .rtp database.

> I would also like to label that residue, I guess that requires the same
> steps?

?label? what do you mean with that?

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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