Re: [gmx-users] Fwd:
On 8/15/17 1:52 AM, saranya wrote: Hi, I have done protein-drug simulations for 100ns. While calculating the hydrogen bond between the protein-drug complex I am getting only 2 hydrogen bonds. The number of H-bond formation is very low I have a question about is there any influence of the drug in my protein? To answer that, you need to do simulations of the apo protein and compare whatever relevant structural metrics there are (not H-bonds, as these tell you about the ligand-protein interactions but nothing about the impact on the protein structure). -Justin -- == 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.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] (Don't know if mail worked last time)Drift with groups+tabulated potential.
Dear GROMACS Community, First of all, if someone got this email twice, I am sorry. It is my first post and I was not sure if it worked. I am trying to do a simulation using a tabulated potential which forces me to use the group cut-off. I get a drift in the conserved quantity of -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules and a Na+ ion. I imagine that eventhough it will soon be deprecated the group cutoff scheme still works correctly. I have tryed to change the parameters without success and in any case the ones I use seem reasonable (in my experience using other programs). The rdfs of the system look normal so I ruled out topology problems. It seems that the problem is in the group cut-off since when I change the tabulated potential for a regular vdw the problem persists. I have followed the instructions of: http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf to implement the tabulated potentials. Is this the kind of energy drift acceptable? I have pasted a copy .mdp Thanks for your help, Sergio Perez-Conesa integrator = md dt = 0.001 nsteps = 10 init-step = 0 cutoff-scheme = group nst-list = 1 verlet-buffer-tolerance = 0.0005 ns-type = grid rlist = 1.3 pbc = xyz coulombtype = PME-switch rcoulomb = 1. rcoulomb-switch = 0.95 pme-order = 4 fourierspacing = 0.1 ewald-rtol = 1.e-5 vdwtype = user rvdw = 1.0 DispCorr = No tcoupl = v-rescale tc-grps = System ;nsttcouple = 1 tau-t = ref-t = 300.0 constraints = all-angles constraint-algorithm = LINCS lincs_iter = 1 lincs_order = 4 energygrps = NA OW energygrp_table = NA OW comm-mode = linear -- 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] how to make molecular model with both ion channel and lipid bilayer?
Dear all, I am trying to make a model of ion channel with cell membrane. Is there a specific software to make this? I mean just the coordination file. VMD can generate the membrane automatically, I can find the 'pdb' files of ion channels, but I have no idea how to combine them. Thanks all, Tong -- 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] how to make molecular model with both ion channel and lipid bilayer?
Charmm-gui.org could help you. Bests, Hadi On Tue, Aug 15, 2017 at 07:55 PM, "Li, Tong" wrote: Dear all, I am trying to make a model of ion channel with cell membrane. Is there a specific software to make this? I mean just the coordination file. VMD can generate the membrane automatically, I can find the 'pdb' files of ion channels, but I have no idea how to combine them. Thanks all, Tong -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List (http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List) before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists (http://www.gromacs.org/Support/Mailing_Lists) * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users (https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users) or send a mail to gmx-users-requ...@gromacs.org (mailto: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.
[gmx-users] Doing restart
#yiv4389709560 blockquote, #yiv4389709560 div.yiv4389709560yahoo_quoted {margin-left:0 !important;border-left:1px #715FFA solid !important;padding-left:1ex !important;background-color:white;} Dear gmx users I stoped my md simulation and now i want to restart it. I use gromacs 2016.3 and issued this command to perform md:Gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.tpr -n index.ndx -o md_0_1.tprGmx mdrun -deffnm md_0_1 To restart simulation i issuedGmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt -appendBut faced to an error: Fatal error: File appending requested, but 2 of the 3 output files are not present or are named differently. For safety reasons, GROMACS-2016 and later only allows file appending to be used when all files have the same names as they had in the original run. Checkpointing is merely intended for plain continuation of runs. For safety reasons you must specify all file names (e.g. with -deffnm), and all these files must match the names used in the run prior to checkpointing since we will append to them by default. If the files are not available, you can add the -noappend flag to mdrun and write separate new parts. For mere concatenation of files, you should use the gmx trjcat tool instead. i refered to google but i couldnt understand well what should i type exactly. would you please help me to restart my md simulation? Thanks in advanceFarial Sent from Yahoo Mail for iPhone -- 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] npt simulation error
Dear Sir I am trying to simulate protein_ligand complex using epsilon = 4 and it is giving the below error *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x* I have no idea how to solve this problem -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu * * Skype: parash.khan2* *Cell: +12085967165* -- 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] npt simulation error
On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: Dear Sir I am trying to simulate protein_ligand complex using epsilon = 4 and it is giving the below error What is epsilon = 4? *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x* I have no idea how to solve this problem Have you Googled it, or gone to the GROMACS error page, where lots of advice lives? ;) -Justin -- == 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.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] npt simulation error
; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 4 On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul wrote: > > > On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote: > >> Dear Sir >> >> I am trying to simulate protein_ligand complex using epsilon = 4 and it is >> giving the below error >> >> > What is epsilon = 4? > > *2 particles communicated to PME rank 4 are more than 2/3 times the cut-off >> out of the domain decomposition cell of their charge group in dimension x* >> >> I have no idea how to solve this problem >> >> > Have you Googled it, or gone to the GROMACS error page, where lots of > advice lives? ;) > > -Justin > > -- > == > > 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.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > -- > 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. > -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu * * Skype: parash.khan2* *Cell: +12085967165* -- 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] positioning molecule at desired location
Dear all, I want to keep a water molecule at a particular position of a protein channel. I need to pull this across the channel and observe the energy diagram by PMF. can anyone tell me how I can keep water molecules at a particular position. 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.
[gmx-users] (no subject)
Hii Everyone I had performed a 100ns protein-ligand (docked complex) simulation with gromacs 5.1.4. The ligand in my case is hydrogen peroxide. I have removed the PBC effect and centered the protein. I have used the following commands: gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc I am analyzing the average distance between the protein and the ligand. I am getting a value of 3.2nm which is too high. Also in the out_1.xtc, after 10ns itself the ligand is moving all around the protein. Unable to understand why its happening!! Please suggest. Thank You Regards Z. Hazarika Research Scholar Tezpur University Tezpur, India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- 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] (no subject)
I suggest check for the appropriate binding pocket. See whether the ligand relocates at some other point in protein or keep to stay away. Also check for the quality of the topology generated. On Wed, Aug 16, 2017 at 10:11 AM, wrote: > Hii Everyone > > I had performed a 100ns protein-ligand (docked complex) simulation with > gromacs 5.1.4. > > The ligand in my case is hydrogen peroxide. > > I have removed the PBC effect and centered the protein. > > I have used the following commands: > > gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc > > gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc > > I am analyzing the average distance between the protein and the ligand. I > am getting a value of 3.2nm which is too high. > > Also in the out_1.xtc, after 10ns itself the ligand is moving all around > the protein. > > Unable to understand why its happening!! > > Please suggest. > > Thank You > > Regards > > Z. Hazarika > Research Scholar > Tezpur University > Tezpur, India > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and destroy > it from your system. Though considerable effort has been made to deliver > error free e-mail messages but it can not be guaranteed to be secure or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. > -- > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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.