[gmx-users] Problem with amidation in pdb2gmx

[Justin A. Lemkul]

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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