[gmx-users] Problem with amidation in pdb2gmx

s4026869 at student.uq.edu.au s4026869 at student.uq.edu.au
Thu Feb 7 15:27:51 CET 2008

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

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.


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?



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