[gmx-users] Pyroglutamic Acid - Topology (pdb2gmx)

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 15 12:50:14 CEST 2009



Christian wrote:
> Hello,
> 
> for my calculations i have to mutate the N-terminal Glutamate into an 
> Pyroglutamate (Pyroglutamic Acid). This modification was done with a modeling 
> program like chimera. 
> After this i changed the AS-name into PGLU (or PGL) and converted 
> the file again with editconf. 
> This file i used to create a pdb2gmx (opls-AA) topology file. 
> 
> The Atomtypes of my Pyroglutamate are fine with Respect to the ffoplsAA.rtp 
> Definitions.
> BUT the Peptide bond between the Pyroglutamate and the next Amino acid (PHE) 
> is 
> broken and the Amide-N of the PHE now has 2 additional Hydrogen's. (H1,H2,H3) 
> So it looks like the new N-Terminus of the Peptide.
> 
> Whats wrong with my Workflow or do i have to change other files or parameters? 
> Is there another possible solution to generate 
> the topology-file ?? (I also tested MKTOP and x2top without success)?
> 
> ---> Here is an extract of the *.pdb-file before pdb2gmx:
> MODEL        1
> ATOM      1  N   PGL     1     -18.120  12.453  -2.596  1.00  0.00
> ATOM      2  H   PGL     1     -17.876  11.927  -3.414  1.00  0.00
> ATOM      3  CA  PGL     1     -17.152  12.709  -1.544  1.00  0.00
> ATOM      4  C   PGL     1     -16.837  11.457  -0.758  1.00  0.00
> ATOM      5  O   PGL     1     -17.526  10.460  -0.910  1.00  0.00
> ATOM      6  CB  PGL     1     -17.870  13.805  -0.712  1.00  0.00
> ATOM      7  CG  PGL     1     -19.376  13.646  -1.039  1.00  0.00
> ATOM      8  CD  PGL     1     -19.338  12.972  -2.377  1.00  0.00
> ATOM      9  OE  PGL     1     -20.298  12.913  -3.130  1.00  0.00
> ATOM     10  HA  PGL     1     -16.216  13.103  -1.975  1.00  0.00
> ATOM     11  HB1 PGL     1     -17.655  13.744   0.367  1.00  0.00
> ATOM     12  HB2 PGL     1     -17.546  14.796  -1.076  1.00  0.00
> ATOM     13  HG1 PGL     1     -19.879  12.966  -0.339  1.00  0.00
> ATOM     14  HG2 PGL     1     -19.906  14.612  -1.059  1.00  0.00
> ATOM     15  N   PHE     2     -15.762  11.500   0.064  1.00  0.00
> ATOM     16  CA  PHE     2     -15.285  10.290   0.734  1.00  0.00
> ATOM     17  C   PHE     2     -16.361   9.695   1.610  1.00  0.00
> ATOM     18  O   PHE     2     -16.475   8.479   1.627  1.00  0.00
> ATOM     19  CB  PHE     2     -14.046  10.561   1.632  1.00  0.00
> ATOM     20  CG  PHE     2     -12.788  10.845   0.796  1.00  0.00
> ATOM     21  CD1 PHE     2     -12.378  12.157   0.528  1.00  0.00
> ATOM     22  CD2 PHE     2     -12.023   9.780   0.307  1.00  0.00
> ATOM     23  CE1 PHE     2     -11.205  12.399  -0.193  1.00  0.00
> ATOM     24  CE2 PHE     2     -10.818  10.021  -0.359  1.00  0.00
> ATOM     25  CZ  PHE     2     -10.423  11.331  -0.640  1.00  0.00
> ATOM     26  HA  PHE     2     -15.007   9.553  -0.038  1.00  0.00
> ATOM     27  HB1 PHE     2     -13.840   9.676   2.257  1.00  0.00
> ATOM     28  HB2 PHE     2     -14.257  11.398   2.315  1.00  0.00
> ATOM     29  HD2 PHE     2     -12.358   8.757   0.448  1.00  0.00
> ATOM     30  HE2 PHE     2     -10.184   9.192  -0.654  1.00  0.00
> ATOM     31  HZ  PHE     2      -9.513  11.517  -1.201  1.00  0.00
> ATOM     32  HE1 PHE     2     -10.896  13.419  -0.402  1.00  0.00
> ATOM     33  HD1 PHE     2     -12.963  12.998   0.883  1.00  0.00
> ATOM     34  H   PHE     2     -15.248  12.350   0.181  1.00  0.00
> .....
> 
> ---> and this is the extract of the resulting *.pdb-file from pdb2gmx:
> 

Did you add PGL to aminoacids.dat?  How did you specify your termini?  What's 
likely happening is that pdb2gmx doesn't know how to deal with PGL properly, so 
it's assuming PHE is the N-terminal residue and is treating it as such.

-Justin

> MODEL        1
> ATOM      1  N   PGL     1     -18.120  12.453  -2.596  1.00  0.00
> ATOM      2  H   PGL     1     -17.876  11.927  -3.414  1.00  0.00
> ATOM      3  CA  PGL     1     -17.152  12.709  -1.544  1.00  0.00
> ATOM      4  HA  PGL     1     -16.216  13.103  -1.975  1.00  0.00
> ATOM      5  CB  PGL     1     -17.870  13.805  -0.712  1.00  0.00
> ATOM      6  HB1 PGL     1     -17.655  13.744   0.367  1.00  0.00
> ATOM      7  HB2 PGL     1     -17.546  14.796  -1.076  1.00  0.00
> ATOM      8  CG  PGL     1     -19.376  13.646  -1.039  1.00  0.00
> ATOM      9  HG1 PGL     1     -19.879  12.966  -0.339  1.00  0.00
> ATOM     10  HG2 PGL     1     -19.906  14.612  -1.059  1.00  0.00
> ATOM     11  CD  PGL     1     -19.338  12.972  -2.377  1.00  0.00
> ATOM     12  OE  PGL     1     -20.298  12.913  -3.130  1.00  0.00
> ATOM     13  C   PGL     1     -16.837  11.457  -0.758  1.00  0.00
> ATOM     14  O   PGL     1     -17.526  10.460  -0.910  1.00  0.00
> ATOM     15  N   PHE     2     -15.762  11.500   0.064  1.00  0.00
> ATOM     16  H1  PHE     2     -15.032  11.874  -0.509  1.00  0.00
> ATOM     17  H2  PHE     2     -16.552  11.276  -0.507  1.00  0.00
> ATOM     18  H3  PHE     2     -16.028  12.178   0.749  1.00  0.00
> ATOM     19  CA  PHE     2     -15.285  10.290   0.734  1.00  0.00
> ATOM     20  HA  PHE     2     -15.007   9.553  -0.038  1.00  0.00
> ATOM     21  CB  PHE     2     -14.046  10.561   1.632  1.00  0.00
> ATOM     22  HB1 PHE     2     -13.840   9.676   2.257  1.00  0.00
> ATOM     23  HB2 PHE     2     -14.257  11.398   2.315  1.00  0.00
> ATOM     24  CG  PHE     2     -12.788  10.845   0.796  1.00  0.00
> ATOM     25  CD1 PHE     2     -12.378  12.157   0.528  1.00  0.00
> ATOM     26  HD1 PHE     2     -12.963  12.998   0.883  1.00  0.00
> ATOM     27  CD2 PHE     2     -12.023   9.780   0.307  1.00  0.00
> ATOM     28  HD2 PHE     2     -12.358   8.757   0.448  1.00  0.00
> ATOM     29  CE1 PHE     2     -11.205  12.399  -0.193  1.00  0.00
> ATOM     30  HE1 PHE     2     -10.896  13.419  -0.402  1.00  0.00
> ATOM     31  CE2 PHE     2     -10.818  10.021  -0.359  1.00  0.00
> ATOM     32  HE2 PHE     2     -10.184   9.192  -0.654  1.00  0.00
> ATOM     33  CZ  PHE     2     -10.423  11.331  -0.640  1.00  0.00
> ATOM     34  HZ  PHE     2      -9.513  11.517  -1.201  1.00  0.00
> ATOM     35  C   PHE     2     -16.361   9.695   1.610  1.00  0.00
> ATOM     36  O   PHE     2     -16.475   8.479   1.627  1.00  0.00
> .....
> 
> Thanks
> Christian
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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



More information about the gromacs.org_gmx-users mailing list