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)." 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.
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