P.R.Anand Narayanan wrote:
----- Forwarded Message ----
*From:* P.R.Anand Narayanan <nandu_coolde...@yahoo.co.in>
*To:* gromacs <gmx-users@gromacs.org>
*Sent:* Mon, 18 January, 2010 12:12:45 PM
*Subject:* Re:Re: Polymer-protein
Dear Gromacs users,
I have to attach a chemical polymer to a protein and when I created
peptide bonds and saved it, the entire format of the pdb file changed.
That is the entire identity of the protein was lost and the pdb file was
saved in the form of ATOMS and not residues.
That is,
"PROTEIN IN ITS PDB FORMAT"-
ATOM 1 N GLY A 3 13.102 19.500 65.823 1.00
35.46 N
ATOM 2 CA GLY A 3 13.351 19.610 64.358 1.00
35.46 C
ATOM 3 C GLY A 3 13.672 18.235 63.779 1.00
35.46 C
ATOM 4 O GLY A 3 12.833 17.341 64.029 1.00
35.46 O
ATOM 5 N ILE A 4 14.789 18.041 63.100 1.00
33.26 N
ATOM 6 CA ILE A 4 15.065 16.703 62.567 1.00
33.26 C
ATOM 7 C ILE A 4 14.891 15.581 63.573 1.00
33.26 C
ATOM 8 O ILE A 4 14.301 14.552 63.227 1.00
33.26 O
ATOM 9 CB ILE A 4 16.488 16.599 61.907 1.00
29.15 C
ATOM 10 CG1 ILE A 4 16.757 15.146 61.417 1.00
29.15 C
AFTER BINDING THE POLYMER TO IT, THE PDB IS NOW SAVED AS:
HETATM 1 N 1 -24.998 12.703 12.925
HETATM 2 C 2 -24.749 12.813 11.460
HETATM 3 C 3 -24.428 11.438 10.881
HETATM 4 O 4 -25.267 10.544 11.131
HETATM 5 H 5 -25.225 13.528 13.462
HETATM 6 H 6 -25.636 13.216 10.970
HETATM 7 H 7 -23.903 13.478 11.291
HETATM 8 H 8 -24.228 12.218 13.362
HETATM 9 H 9 -25.871 12.195 12.948
HETATM 10 N 10 -23.311 11.244 10.202
That is, it is saved as single atoms and not as RESIDUES and hence the
entire protein identity is lost. Are there any solutions to this or can
I Use the same in gromacs??????? If yes, how can I use it in the pdb2gmx
command????
What program did you use to create this new PDB file? It looks like it severely
crippled the file, changing just about everything about it. There is certainly
no way to use this .pdb file, since there aren't even any residue names defined
in it.
-Justin
Please help,
Thanking you,
regards,
Anand
------------------------------------------------------------------------
The INTERNET now has a personality. YOURS! See your Yahoo! Homepage
<http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/>.
------------------------------------------------------------------------
The INTERNET now has a personality. YOURS! See your Yahoo! Homepage
<http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/>.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
