Re: [gmx-users] how to parametrize Phos. Thr TPO
There is already a user contribution in the gromacs page named ffG43a1p, that is based in the force field ffG43a1 and also includes phosphorilated serine end threonine. However, is exciting doing it for yourself. Mensaje citado por nahren manuel : > Dear Gromacs Users, > > I am trying to simulate a protein whose Thr residues is phosphorylated. > I did the following based on the earlier query regarding the same > > here is how I did it for phosphorylated Threonine. > > > 1) open the appropriate .rtp file e.g. ffG43a1.rtp > 2) make a copy of the existing entry for the residue > you want to phosphorylate it. > > here are the notes I made as I did it...comments > welcome if anyone > doesnt like how I did it! > > ; TPO which follows is phosphorylated Threonine and > was derived thus: > ; 1) take THR entry > ; 2) add P, O1P, O2P, O3P atoms > ; 3) remove HG1 atom > ; 4) assign partial charges to give an overall > molecule -2 charge > ; with this charge localised on the Phosphate > group. > ; 5) add bonds for OG1 to P and the OxPs. took bond > tpyes from [ DADE ] > ; 6) likewise took angle types from [ DADE ] > ; 7) removed final dihedral which contained H1 (had > considered changing > it for > ; P but dont want to limit Phoshphate group too > much) > > 3) you will need to add the new residue to the file > aminoacids.dat if > you want the residue to be recognised as part of the > protein in > subsequent analysis. Make sure you increment the count > on the top line > of aminoacids.dat. dont put any comments in > aminoacids.dat becuase it > has unpredictable effects on results. > 4) update the hydrogen database entry too if you are > expecting pdb2gmx > or protonate to work properly. > > I *think* that was it...! > > Paul Barrett > > > but i get the following error > * * * * * > Generated 380 of the 1326 non-bonded parameter combinations > ERROR 0 [file "top_A.itp", line 16530]: > No default Proper Dih. types > ERROR 0 [file "top_A.itp", line 16531]: > No default Proper Dih. types > Excluding 3 bonded neighbours for Protein_A 1 > Excluding 3 bonded neighbours for Protein_B 1 > NOTE: > System has non-zero total charge: -1.96e+00 > > processing coordinates... > double-checking input for internal consistency... > renumbering atomtypes... > converting bonded parameters... > # G96BONDS: 5789 > # G96ANGLES: 8462 > # PDIHS: 3040 > # IDIHS: 2893 > # LJ14: 9248 > > --- > Program grompp, VERSION 3.3.2 > Source code file: grompp.c, line: 1182 > > Fatal error: > There were 2 errors in input file(s) > --- > > "Ich Bin Ein Berliner" (J.F. Kennedy) > * * * * * * > > Kindly advice > nahren > > > > > > Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] how to parametrize Phos. Thr TPO
nahren manuel wrote: but i get the following error * * * * * Generated 380 of the 1326 non-bonded parameter combinations ERROR 0 [file "top_A.itp", line 16530]: No default Proper Dih. types ERROR 0 [file "top_A.itp", line 16531]: No default Proper Dih. types Then you haven't added all of the proper dihedrals for that particular molecule (phosphates are tricky). There is a parameter set (ffG43a1p) that has a properly-derived set of parameters for phosphorylated amino acids in the User Contributions on the web site. I recall that not all of the formatting was quite right in these files (they were designed for use with Gromacs 3.1.x, IIRC), so if you encounter errors you can contact me off-list and I can send you re-formatted files that I have gotten to work. -Justin Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 NOTE: System has non-zero total charge: -1.96e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 5789 # G96ANGLES: 8462 # PDIHS: 3040 # IDIHS: 2893 # LJ14: 9248 --- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: 1182 Fatal error: There were 2 errors in input file(s) --- "Ich Bin Ein Berliner" (J.F. Kennedy) * * * * * * Kindly advice nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Justin A. Lemkul Graduate Research Assistant 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
[gmx-users] how to parametrize Phos. Thr TPO
Dear Gromacs Users, I am trying to simulate a protein whose Thr residues is phosphorylated. I did the following based on the earlier query regarding the same here is how I did it for phosphorylated Threonine. 1) open the appropriate .rtp file e.g. ffG43a1.rtp 2) make a copy of the existing entry for the residue you want to phosphorylate it. here are the notes I made as I did it...comments welcome if anyone doesnt like how I did it! ; TPO which follows is phosphorylated Threonine and was derived thus: ; 1) take THR entry ; 2) add P, O1P, O2P, O3P atoms ; 3) remove HG1 atom ; 4) assign partial charges to give an overall molecule -2 charge ; with this charge localised on the Phosphate group. ; 5) add bonds for OG1 to P and the OxPs. took bond tpyes from [ DADE ] ; 6) likewise took angle types from [ DADE ] ; 7) removed final dihedral which contained H1 (had considered changing it for ; P but dont want to limit Phoshphate group too much) 3) you will need to add the new residue to the file aminoacids.dat if you want the residue to be recognised as part of the protein in subsequent analysis. Make sure you increment the count on the top line of aminoacids.dat. dont put any comments in aminoacids.dat becuase it has unpredictable effects on results. 4) update the hydrogen database entry too if you are expecting pdb2gmx or protonate to work properly. I *think* that was it...! Paul Barrett but i get the following error * * * * * Generated 380 of the 1326 non-bonded parameter combinations ERROR 0 [file "top_A.itp", line 16530]: No default Proper Dih. types ERROR 0 [file "top_A.itp", line 16531]: No default Proper Dih. types Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 NOTE: System has non-zero total charge: -1.96e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 5789 # G96ANGLES: 8462 # PDIHS: 3040 # IDIHS: 2893 # LJ14: 9248 --- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: 1182 Fatal error: There were 2 errors in input file(s) --- "Ich Bin Ein Berliner" (J.F. Kennedy) * * * * * * Kindly advice nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
