[gmx-users] Problem with amidation in pdb2gmx

[Justin A. Lemkul]

Sorry, clicked 'send' too soon.  How was this version of Gromacs compiled?  I
remember submitting a bugzilla not too long ago about a similar problem, and it
ended up being that the Ubuntu package was broken.  Re-compiling from source
fixed the problem.  The -ter response was a knee-jerk reaction, as a related
problem is somewhere in the list archive.

-Justin

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> Quoting s4026869 at student.uq.edu.au:
>
> > Hello all,
> >
> > I have a protein with missing N- and C- terminus residues. I am
> > simulating a complex. To avoid in-silico charge interactions at the
> > wrong places due to the missing residues I have performed acetylation
> > and amidation.
> >
> >
> > When running pdb2gmx (GMX331) I experience a problem -
> >
> >
> > pdb2gmx -f blah.pdb -o blah.gro -p blah.top -water spc -ter -ignh -merge
>
> Are you choosing 'none' for your termini?
>
> -Justin
>
> >
> >
> > Fatal error:
> > Atom H not found in residue 177 while adding improper
> >
> >
> > 177 is the number of the NH2 cap after re-numbering of the pdb file.
> >
> >
> > EXTRACT FROM THE PDB FILE -
> >
> > .....
> > ATOM   1382  N   NH2 A 181      15.061  41.575  44.283  0.00  0.00
> > N
> > ATOM   1383  H1  NH2 A 181      14.812  41.813  45.232  0.00  0.00
> > H
> > ATOM   1384  H2  NH2 A 181      16.038  41.447  44.027  0.00  0.00
> > H
> > ....
> >
> >
> > The ffG53a6.rtp has the NH2 as -
> >
> >
> > [ NH2 ]
> >   [ atoms ]
> >       N    NT   -0.83    0
> >       H1    H   0.415    0
> >       H2    H   0.415    0
> >   [ bonds ]
> >        N    H1  gb_2
> >        N    H2  gb_2
> >       -C    N   gb_9
> >   [ angles ]
> >       -O -C N  ga_33
> >       -CA -C N ga_19
> >       -C N H1  ga_23
> >       -C N H2  ga_23
> >       H1 N H2  ga_24
> >   [ dihedrals ]
> >      -CA -C N H1 gd_14
> >   [ impropers ]
> >      -C -O N -CA gi_1
> >       N  H H  -C gi_1
> >
> >
> > Am I missing something?
> >
> > I reproduce this error with GMX332.
> >
> > However, if I use pdb2gmx with v3.2.1, pdb2gmx does not complain !
> >
> >
> > Does anyone have any ideas/fixes?
> >
> >
> > Cheers
> >
> > Mitch
> >
> >
> >
> > _______________________________________________
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> >
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================