[gmx-users] Capping (neuralising) of peptide

[Alok]

Hello
      As i generated the pdb file of tripeptide (GPG) using insight. After
capping (neuralising) of that peptide on both N and C terminal (i changed
glycine’s N terminal to NH2 and second glycine’s C terminal to COOH).
But now i am geeting another problem as these GLY residues are not define
in .rtp file.so following error comes up after pdb2gmx.




Select the Force Field:
 0: GROMOS96 43a1 Forcefield (official distribution)
 1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
 2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) 3:
OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 4: Gromacs Forcefield (see manual)
 5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 124 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 16 residues with 124 atoms

  chain  #res #atoms
  1 ' '    16    124

WARNING: there were 0 atoms with zero occupancy and 1 atoms with
         occupancy unequal to one (out of 124 atoms). Check your pdb file.
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb

Back Off! I just backed up peptide.top to ./#peptide.top.7#
Processing chain 1 (124 atoms, 16 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 19 hydrogen bonds
Fatal error: Atom HA1 in residue GLY 1 not found in rtp entry with 5 atoms
             while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh will ignore all hydrogens in the input.




so now what I have to do now? should i define these GLY residue in .rtp
file?? Or anything else??

i am attaching  pdb file also.




ATOM      1  N   GLY     1      15.055  26.899  27.745  1.00  0.00
  N
ATOM      2  CA  GLY     1      14.262  27.999  27.204  1.00  0.00
  C
ATOM      3  C   GLY     1      14.753  29.328  27.725  1.00  0.00
  C
ATOM      4  O   GLY     1      15.669  29.411  28.537  1.00  0.00
  O
ATOM      5 1H   GLY     1      15.783  27.276  28.371  1.00  0.00
  H
ATOM      6 2H   GLY     1      14.444  26.262  28.276  1.00  0.00
  H
ATOM      7 1HA  GLY     1      14.313  28.000  26.100  1.00  0.00
  H
ATOM      8 2HA  GLY     1      13.198  27.873  27.476  1.00  0.00
  H
ATOM      9  N   PRO     1B     14.138  30.394  27.257  1.00  0.00
  N
ATOM     10  CA  PRO     1B     14.502  31.745  27.655  1.00  0.00
  C
ATOM     11  C   PRO     1B     14.016  32.068  29.078  1.00  0.00
  C
ATOM     12  O   PRO     1B     12.967  31.584  29.504  1.00  0.00
  O
ATOM     13  CB  PRO     1B     13.737  32.594  26.628  1.00  0.00
  C
ATOM     14  CG  PRO     1B     12.506  31.737  26.294  1.00  0.00
  C
ATOM     15  CD  PRO     1B     13.059  30.311  26.295  1.00  0.00
  C
ATOM     16  HA  PRO     1B     15.585  31.876  27.616  1.00  0.00
  H
ATOM     17 1HB  PRO     1B     13.474  33.584  27.007  1.00  0.00
  H
ATOM     18 2HB  PRO     1B     14.352  32.706  25.731  1.00  0.00
  H
ATOM     19 1HG  PRO     1B     11.763  31.839  27.088  1.00  0.00
  H
ATOM     20 2HG  PRO     1B     12.057  32.005  25.335  1.00  0.00
  H
ATOM     21 1HD  PRO     1B     12.312  29.578  26.607  1.00  0.00
  H
ATOM     22 2HD  PRO     1B     13.464  30.046  25.315  1.00  0.00
  H
ATOM     23  N   GLY     1C     14.726  32.860  29.852  1.00  0.00
  N
ATOM     24  CA  GLY     1C     14.238  33.314  31.151  1.00  0.00
  C
ATOM     25  C   GLY     1C     13.769  34.748  31.082  1.00  0.00
  C
ATOM     26  O   GLY     1C     13.445  35.378  32.087  1.00  0.00
  O
ATOM     27  H   GLY     1C     15.654  33.172  29.532  1.00  0.00
  H
ATOM     28 1HA  GLY     1C     13.403  32.675  31.489  1.00  0.00
  H
ATOM     29 2HA  GLY     1C     15.036  33.230  31.910  1.00  0.00
  H
ATOM     30  O   OH      2      13.704  35.373  29.853  1.00  0.00
  O
ATOM     31  HO  OH      2      13.391  36.273  29.966  1.00  0.00
  H



Thanks!

       Alok