Thank you dear justin. I'll read the paper. But practically it is mentioned that (for simulation) it has 51 residues which exactly equal to A,B chain. And i hope you answer the question about protonating ...." Residues B23-B30 were removed from insulin 43 residues. The C-terminal carboxyl groups and all the charged residues were set to be protonated to simulate the protein structures under acidic conditions. Parameterized force field parameters for protonated C-terminal carboxyl groups were used (Hong et al., 2012)." I didn't protonate the molecule, so when i used grompp, my system had not integer charges, is it because of i ignore the polar groups and didn't protonate carboxyl groups?
Best On Wed, 29 Aug 2018, 22:46 Justin Lemkul, <jalem...@vt.edu> wrote: > > > On 8/29/18 2:13 PM, Nick Johans wrote: > > Thank you so much Iris. > > want to simulate a protwin interaction with nanotube. The question is > the > > pdb file structure. As i have not simulate protein before and i know that > > insulin has 2 chains the question is that why in pdbcode(3e7y) insulin > has > > 4 chain? > > > > You need to read the paper associated with that crystal structure as > well as header information in the PDB file as to why this is. A crystal > complex is not necessarily the same as a functional complex. > > -Justin > > > On Wed, 29 Aug 2018, 22:00 Smith, Iris, <smit...@ccf.org> wrote: > > > >> Hi Nick, > >> > >> I think the big question is what are you trying to simulate – what is > your > >> goal? It is critical that you now your protein (e.g. how was it > >> crystalized, any missing atoms, missing residues, hetero atoms, > ligands). I > >> think prior to building your system you should first understand your > goal > >> and get a stronger foundation on MDS as well as the forcefiled you > require > >> to model your system, this will help you better understand the flags for > >> each gmx command. > >> > >> I would start with first reading the gromacs manual and re-reading the > >> reference paper associated with your PDB. Present your hypothesis and > >> goal(s) to your colleagues – this will help you formulate a > >> hypothesis-driven project. > >> > >> Iris > >> > >> > >> > >> > [/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1833992660] > >> > >> Iris Nira Smith | Postdoctoral Fellow | Genomic Medicine Institute > >> Cleveland Clinic | 9500 Euclid Ave. / NE5-255 | Cleveland, OH > 44195 | > >> (216) 445-7885 > >> > >> > >> > >> > >> From: <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > >> Nick Johans <johans.nic...@gmail.com> > >> Reply-To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > >> Date: Wednesday, August 29, 2018 at 11:36 AM > >> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > >> Subject: [BULK][EXT] Re: [gmx-users] PDB code > >> > >> Sorry, i have just removed C,D chains by pymol and then started > >> simulating(without adding any terminal or H,...)... but after grompp, > the > >> system had charges and were not integer. Is it because of i didn't add > >> terminals? I use AMBER99SB forcefield and as you know it doesn't work > with > >> -ter but i have read paper which is said( that's my reference paper); > >> " Residues B23-B30 were > >> removed from insulin 43 residues. The C-terminal carboxyl groups and all > >> the charged residues were set to be > >> protonated to simulate the protein structures under acidic conditions. > >> Parameterized force field parameters for > >> protonated C-terminal carboxyl groups were used (Hong et al., 2012)." > >> > > And how should protonate molecule in AMBER ff? > > > > What does it mean "protonated" ? How they add H when they have used AMBER > >> forcefield? > >> Would you please help me? > >> > >> Best regards > >> On Wed, 29 Aug 2018, 19:50 Nick Johans, <johans.nic...@gmail.com> > wrote: > >> > >>> Hi, > >>> > >>> I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology > file > >>> of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When > >> you > >>> google it, it is mentioned that insuline has 2 chains named A,B. So why > >>> it's pdb code has 4 chains? Are they couple of each other? If yes and i > >>> should remove C,D chains, is there any tool to remove them standardly > >>> ;)(not manually)? > >>> > >>> How about Zn, Cl atoms there? Should i remove all nonbonded atoms when > >>> starting simulation? > >>> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List< > >> > https://protect-us.mimecast.com/s/TLbLCG6xpNtGGMziQt_Dy?domain=gromacs.org > > > >> before posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists< > >> > https://protect-us.mimecast.com/s/-YXNCJ6Avkt55YjUvCgAi?domain=gromacs.org > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users< > >> > https://protect-us.mimecast.com/s/HUA1CKrBwlimmnRSGaanT?domain=maillist.sys.kth.se > > > >> or send a mail to gmx-users-requ...@gromacs.org. > >> > >> > >> =================================== > >> > >> > >> Please consider the environment before printing this e-mail > >> > >> Cleveland Clinic is currently ranked as the No. 2 hospital in the > country > >> by U.S. News & World Report (2017-2018). Visit us online at > >> http://www.clevelandclinic.org for a complete listing of our services, > >> staff and locations. Confidentiality Note: This message is intended for > use > >> only by the individual or entity to which it is addressed and may > contain > >> information that is privileged, confidential, and exempt from disclosure > >> under applicable law. If the reader of this message is not the intended > >> recipient or the employee or agent responsible for delivering the > message > >> to the intended recipient, you are hereby notified that any > dissemination, > >> distribution or copying of this communication is strictly prohibited. If > >> you have received this communication in error, please contact the sender > >> immediately and destroy the material in its entirety, whether > electronic or > >> hard copy. Thank you. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.