[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
>
>
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--
========================================
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
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