Re: [gmx-users] Implicit and Explicit solvation
On 12/23/16 10:22 PM, Syed Azeem wrote: Thanks Tyugashev for your response. It was a reviewer suggestion to run our protein-peptide docked complex in a continuum solvent and compute their free energies of association. After this, I came across MMPBSA and its GROMACS tool g_mmpbsa. Is this not based on Implicit solvation? How can I perform it to validate my docking? MM/PBSA is a post-processing (analysis) method in which you provide existing snapshots and the MM energy is combined with a PBSA estimate of solvation free energy to give the free energy of the system. The (unofficial) g_mmpbsa tool does this. It does not require additional simulations. -Justin Thanks in advance Azeem From: Timofey Tyugashev To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Implicit and Explicit solvation Message-ID: <17ce8acf-3566-f23f-3931-77ed00c37...@niboch.nsc.ru> Content-Type: text/plain; charset=UTF-8; format=flowed Implicit solvation treats solvent as a continuous medium (a kind of modifier for , while explicit one treats it as a set of explicit (surprise!) particles. I guess you can start reading from relevant Wikipedia articles. Implicit is way faster to compute, the system itself also settles far quicker, but it's considered more inaccurate and harder to optimize for GPU. It's also possible to have a hybrid approach, when the whole system is solvated implicitly, but select solvent molecules are explicitly included in the model. In GROMACS implicit solvent is depreciated, so you should either use explicit solvent, or pick a different MD engine if you want implicit. 23.12.2016 18:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se ?: Message: 1 Date: Fri, 23 Dec 2016 16:25:33 +0530 From: Syed Azeem To: "gromacs.org_gmx-users" Subject: [gmx-users] Implicit and Explicit solvation Message-ID: Content-Type: text/plain; charset=UTF-8 Hi all, What's the difference between Implicit and Explicit solvation? Is there any difference in setting up the system for simulation? Which is computationally effiecient? Thanks in advance Azeem -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] TIP3 water problem
On 12/25/16 8:01 AM, nikol...@spbau.ru wrote: Ok, but how to craft it? I tried adding line in the end: TIP3 76 but that failed to the wrong residue type... Water is called "SOL" in GROMACS. Always check the [moleculetype] name in the .itp file before hacking the system topology. -Justin Hi, That's fine, but you still don't need pdb2gmx to try to generate topologies for any kind of water. Use pdb2gmx to generate your protein itp file, and then craft the top file to match the contents of the structure file that e.g had crystallographic water before you solvated it also. The tools are flexible and powerful, and not everything has to follow the simple linear examples in tutorials :-) Mark On Sun, 25 Dec 2016 09:37 wrote: Oh, sorry, these were only charges, masses etc, no coords. I wish I could use only gromacs waters, but I use extra software for prediction of crystallographic waters... On 12/23/16 3:30 AM, nikol...@spbau.ru wrote: Well, as I understand I need to do the following: Provide pdb file with different chains for protein and waters; gmx pdb2gmx -f 3WQJ.pdb -o 3wqj.gro then go into the topol_Other_chain_X.itp; delete everything that after the atom coords; There are no coordinates in any .itp file, so I don't follow. then run everything in the same way. I have tried this and it seems to work, I just want to make sure that I am doing everything right. Basically, my recommendation is: don't feed waters to pdb2gmx. Solvate with normal GROMACS tools and use the stock water topology, which accounts for everything. -Justin Anyway, thank you for help! Dmitrii. On 12/20/16 2:41 PM, nikol...@spbau.ru wrote: Hi, all! I am working with the protein structure with internal waters of TIP3 type, and running grompp ends with an error of "No default U-B types", as I understand because of some internal inconsistency between atom types (H1, H2 and OH2 in my tip3, HW1, HW2, OW in sol). I tried to rename atoms in both topol.top and .gro files, add extra .itp file in charmm27.ff, nothing worked. However, this problem has already been mentioned here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/087725.html and the solution involved modifying top file (add waters information manually). Is it really the only solution of this problem? Because as I understand I need to insert manually all the charges, angles, bond lenths for all the water molecules. And it seems quite a problem, if I want to run more than 1 system. Water molecules should not have [bonds] and [angles] directives because they should be treated as rigid via SETTLES. If your topology has explicit bonds and angles, remove them and re-process the coordinates with pdb2gmx to prevent this spurious assignment. Then just #include "tip3p.itp" and list the waters in [molecules]. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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://ww
Re: [gmx-users] CG-MD to study the conformational changes of proteins...
Dear Gromacs Users, I have a insilico model of Mycobacterium cell wall (surface) protein which has no transmembrane helices.Which Gromacs tutorials should I follow for MD studies to know about its conformational stability and latter for protein - ligand studies. Kindly guide me Thanking you with regards V.G.Shanmuga Priya On Mon, Dec 26, 2016 at 11:06 PM, Dariush Mohammadyani < d.mohammady...@gmail.com> wrote: > Hi Quyen, > > Although Martini is a good CG force field for a system contains lipids and > proteins, it still needs some improvements to capture conformational > changes (especially large changes). > Is there any hybrid model available (and ready to use) for such a system? > > > Regards, > Dariush > > On Mon, Dec 26, 2016 at 11:23 AM, Quyen V. Vu wrote: > > > Nikhil say: > > > > I would like to study the conformational study of proteins (Amyloid beta) > > in presence of lipid bilayers and other molecules. Can anyone tell me the > > possibility of Coarse-grained molecular dynamics for this study, since > > all-atom MD need more time and my system contains more atoms, so I'm > > thinking to go for CGMD. in CG-MD can we do the same analysis as in > > All-atom MD.? > > > > > > You need to find a force field that support for protein coarse-grain > model > > > > such as Martini: http://cgmartini.nl/ > > > > to save simulation time you can you CG model or hybrid model( result > > better than CG model because a important region > > > > is treated as standard MD, less important region is use CG model > > -- > > 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. > -- 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.
Re: [gmx-users] CG-MD to study the conformational changes of proteins...
Hi Quyen, Although Martini is a good CG force field for a system contains lipids and proteins, it still needs some improvements to capture conformational changes (especially large changes). Is there any hybrid model available (and ready to use) for such a system? Regards, Dariush On Mon, Dec 26, 2016 at 11:23 AM, Quyen V. Vu wrote: > Nikhil say: > > I would like to study the conformational study of proteins (Amyloid beta) > in presence of lipid bilayers and other molecules. Can anyone tell me the > possibility of Coarse-grained molecular dynamics for this study, since > all-atom MD need more time and my system contains more atoms, so I'm > thinking to go for CGMD. in CG-MD can we do the same analysis as in > All-atom MD.? > > > You need to find a force field that support for protein coarse-grain model > > such as Martini: http://cgmartini.nl/ > > to save simulation time you can you CG model or hybrid model( result > better than CG model because a important region > > is treated as standard MD, less important region is use CG model > -- > 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.
Re: [gmx-users] CG-MD to study the conformational changes of proteins...
Nikhil say: I would like to study the conformational study of proteins (Amyloid beta) in presence of lipid bilayers and other molecules. Can anyone tell me the possibility of Coarse-grained molecular dynamics for this study, since all-atom MD need more time and my system contains more atoms, so I'm thinking to go for CGMD. in CG-MD can we do the same analysis as in All-atom MD.? You need to find a force field that support for protein coarse-grain model such as Martini: http://cgmartini.nl/ to save simulation time you can you CG model or hybrid model( result better than CG model because a important region is treated as standard MD, less important region is use CG model -- 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.
[gmx-users] CG-MD to study the conformational changes of proteins...
I would like to study the conformational study of proteins (Amyloid beta) in presence of lipid bilayers and other molecules. Can anyone tell me the possibility of Coarse-grained molecular dynamics for this study, since all-atom MD need more time and my system contains more atoms, so I'm thinking to go for CGMD. in CG-MD can we do the same analysis as in All-atom MD.? -- Regards, Nikhil Maroli -- 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.
