[gmx-users] Energetics of ion and subatrate binding sites

Dear Gromacs Users, I have simulated a protein with different ions and same substrate bound to it in POPC lipid bilayer using Groamcs 4.5.4. The ion binding and substrate binding sites are coupled. After Md simulation we see a reorganization of these sites. Now, we are trying to calculate the ener

Re: [gmx-users] Occupancy for a distance cut off

Thank you!! On Mon, Feb 11, 2013 at 8:29 PM, Justin Lemkul wrote: > > > On 2/11/13 9:16 PM, ram bio wrote: >> >> Hi Justin, >> >> Thanks for the suggestion. >> >> I executed the following command: >> >> g_dist -f n101c2naclprod2-12nsv

Re: [gmx-users] Occupancy for a distance cut off

, Justin Lemkul wrote: > > > On 2/11/13 6:15 PM, ram bio wrote: >> >> Dear Gromacs Users, >> >> I have a run a MD simulation on protein bound with ligand and ions >> using Gromacs 4.5.4. I am able to calculate the distances between ions >> and coordinatin

[gmx-users] Occupancy for a distance cut off

Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for the occupancy for a cut off distance (3.

[gmx-users] barium ion simulation

Dear Gromacs Users, I am trying to simulate a protein in lipid bilayer with a barium ion binding pocket in it, with Charmm27 FF in gromacs 4.5.4. I found that barium ion is not included under charmm27 ff ions.itp. I was wondering if there is any way to simulate protein with barium bound using grom

Re: [gmx-users] xmgrace graphs

Instead of file1 and file2 use ur file name. >> > > Distance plots produced by g_dist have four data sets (distance and x,y,z > components) so plotting in this way can be quite messy. Leave out the -nxy > if you want to only plot the total distance and not the remaining (

[gmx-users] xmgrace graphs

Dear Gromacs users, I am trying to find inter atomic distances between ligand atoms and protein residues using Gromacs commands and could generate individual xvg files, but could not figure out how to merge or show all the xvg files in one graph using xmgrace. Cold you please suggest? Thanks and

[gmx-users] Ca ion simulation incorporated in protein structure

Dear Gromacs Users, I am trying to simulate a modeled protein -ligand complex in lipid bilayer using Gromacs 4.5.4 with Charmm27 FF. For my project purpose which is to see the effect of substitution of ions (Ca instead of Na ions) in the protein structure on protein ligand interactions , I have m

[gmx-users] charmm 27 FF mdp query

Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so

[gmx-users] charmm 27 gromacs version mdp query

Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so

Re: [gmx-users] unknown cmap torsion between atoms

that could be reason? moreover, grompp also throws error as no default U-B types along with unknown CMAP torsion. Could you please diagnose where the problem exists in my procedure and let me know. Thanks Pramod On Mon, Oct 31, 2011 at 9:57 PM, Mark Abraham wrote: > On 1/11/2011 1:24 PM, ram

[gmx-users] unknown cmap torsion between atoms

Dear Gromacs users, I have built a protein embedded in popc bilayer and executed pdb2gmx using charmm27 ff on the system and the toplogy file was created without errors, but when wanted to minimise the system with grompp i am getting an error as : unknown cmap torsion between atoms 8377 8379 8381

[gmx-users] POPC bilayer with Charmmff

Dear Gromacs users, I have downloaded the POPC bilayer molecular coordinates with charmmff equilibrated from Dr. Klauda's website. In this site it is mentioned Note: If you run these simulations in NAMD you MUST use NAMD 2.7b3 with vdw ForceSwitching turned on; what does vdw ForceSwitching turne

[gmx-users] pdb2gmx charmm topology lipid

estions to fix this error. Thanks, Pramod On Wed, Oct 12, 2011 at 8:21 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks. >> >> The POPC bilayer i am using is with berger lipids, corrected for dihedrals >> so as

Re: [gmx-users] mktop

layer structure for embedding the protein and use the related CHARMM FF parameterised itp in the topology file in gromacs for MD simulation. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul wrote: > > > ram bio wrote: > >> Dear Justin, >>

Re: [gmx-users] mktop/swissparam

ing toplogies. > > Please let me know your comments and suggestions regarding the procedure > followed and the itp files usage for gromacs MD simulations. > > Thanks in advance, > > Pramod > > > > On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul wrote: > >> >&

Re: [gmx-users] mktop

cs MD simulations. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul wrote: > > > ram bio wrote: > >> Dear Justin, >> >> As i generated the protein-ligand docked complex using opls FF, for the >> consistency, i am trying to use o

Re: [gmx-users] mktop

d On Wed, Oct 12, 2011 at 1:28 PM, Justin A. Lemkul wrote: > > > ram bio wrote: > >> Dear Justin, >> >> Thanks for the information. >> >> Initially, i just wanted to run a simulation of protein-ligand in water >> solvent . I renamed the topology.

Fwd: [gmx-users] mktop

.gro -p topol.top -o ions.tpr I have attached the topol.top, ligand.itp files for your information, Please let me know your suggestions to fix this error. Thanks, Pramod On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul wrote: > > > ram bio wrote: > >> Dear Gromacs Users, &

[gmx-users] mktop

Dear Gromacs Users, I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is available for merging t

[gmx-users] make_ndx unable to save

Dear Gromacs Users, I have simulated a protein -ligand complex in the popc bilayer and while analysing the results i want to find distance between two residues in the protein during simulation. For that I think I have to use g_hbond command by creating an index.file containing the new groups, but

Re: [gmx-users] RHEL OS, g_mdrun

is difficult now to figure out why I could not use g_mdrun_openmpi, even though the file exists in the path:/usr/lib64/openmpi/bin/g_mdrun_openmpi Ram On Wed, May 18, 2011 at 3:00 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Gromacs Users, >> >> I

[gmx-users] RHEL OS, g_mdrun

Dear Gromacs Users, I am trying to run a gromacs mdrun job (pbs script) on the cluster (RHEL operating system) using the recently installed gromacs version 4.5.3, but i think i could not run it paralleled on the nodes, as it is taking a long time to finish the job. The information regarding the

Re: [gmx-users] protein movement in lipid bilayer during simulation

Dear Justin, Thanks for the suggestion. Best, Ram On Thu, Jan 27, 2011 at 6:46 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Gromacs Users, >> >> I am performing an all-atom simulation of protein ligand complex in >> lipid bilayer , but aft

[gmx-users] protein movement in lipid bilayer during simulation

Dear Gromacs Users, I am performing an all-atom simulation of protein ligand complex in lipid bilayer , but after around 100ns, I see that the protein started moving in one dimension in the lipid bilayer that is it is not in the centre, I want the position of the protein fixed through out the simu

[gmx-users] cannot rename checkpoint file

Dear Gromacs users, I am running an all-atom simulation of protein-ligand complex in lipid bilayer on a server, while running the job after some time, my job terminates with an error as under: Program mdrun, VERSION 4.0.3 Source code file: checkpoint.c, line: 859 File input/output error: Cannot

Re: [gmx-users] Re: tpbconv extension

;> >> Hi Justin and Berk, >> >> Thanks for the suggestions. >> >> I am using gromacs 4.0.7 single precision, and would like to extend my >> run each time by 1 microsec as it fits into the wall time on the >> server for my system. >> Please suggest. >&

Re: [gmx-users] Re: tpbconv extension

: > > > ram bio wrote: >> >> Hi Justin, >> >> The command was: >> >> tpbconv -s memb12extnr42000ns.tpr -extend 100 -o >> memb12extnr43000ns.tpr >> > > Try using -nsteps instead.  There are issues with -extend and -until (bad > ro

Re: [gmx-users] Re: tpbconv extension

Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Gromacs users, >> >> I am running a CG simulation fo

[gmx-users] Re: tpbconv extension

. Not writing tpr file Please give your suggestions to overcome this error. Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio wrote: > Dear Gromacs users, > > I > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] tpbconv extension

Dear Gromacs users, I -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interfa

[gmx-users] swiss param query,

Dear Gromacs Users, I have generated the topology and parameters files for my ligand through swiss param site. Now i am trying to run a simulation of protein ligand complex in POPC bilayer using OPLS force field in Gromacs, but when I am using the grompp command in gromacs for tpr generation I am

[gmx-users] trjcat : Magic Number Error in XTC file (read 0, should be 1995)

Subject: trjcat : Magic Number Error in XTC file (read 0, should be 1995) Dear Gromacs Users, I am trying to cat the .xtc files using the trjcat option in gromacs, but i am getting an error Program gmxcheck, VERSION 4.0.7 Source code file: xtcio.c, line: 85 Fatal error: Magic Number Error in XT

[gmx-users] inversion of lipid bilayer with water in the centre

Dear Gromacs Users, I have a lipid bilayer with me and I would like to simulate a system by keeping the water molecules with proteins in it and lipid surrounding the water on both sides, can any body suggest me please... Thanks Ram -- gmx-users mailing listgmx-users@gromacs.org http://list

Re: [gmx-users] coarse grain dynamics

thanks all for the discussion. On Tue, May 25, 2010 at 5:42 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Thanks for the comments and info, but is there any way to take a >> particular  frame for eg. the last frame  of CG simulation and extend >> the run

Re: [gmx-users] coarse grain dynamics

t; most likely NOT be able to draw conclusions from it. > > Otherwise, everyone would run really fast simulations in CG, then reconstruct > their systems afterward. :) > > > > Quoting "Justin A. Lemkul" : > >> >> >> ram bio wrote: >> > than

Re: [gmx-users] coarse grain dynamics

>> > grain methodology you didn't include all the atoms, so you didn't >> > included hydrogens. So now you can not see them, of course. They are not >> > there. >> > >> > If you need to "know the hydrogen bond interactions" you need to do so

[gmx-users] coarse grain dynamics

Dear Gromacs Users, I have done coarse grain simulation for 2 peptides in bilayer for 1000ns, and now i would like to know the hydrogen bond interactions between these two peptides. Please let me know how to do this, i can visualize the trajectory in VMD, but unable to calculate the hydrogen bondi

Re: [gmx-users] conversion of desmond trajectory files into gromacs

Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole wrote: > > VMD reads Desmond trajectories and writes GMX format ... > Rests the topology to deal with ... > > On Apr 16, 2010, at 4:15 PM, ram bio wrote: > >> Dear

[gmx-users] conversion of desmond trajectory files into gromacs

Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] Multiprotein lipid bilayer

hi justin, will try that thanks Ram On Thu, Mar 4, 2010 at 4:51 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> HI Justin, >> >> Thanks for the info. >> >> I have followed your tutorial earlier, it really works, and that was >>

Re: [gmx-users] Multiprotein lipid bilayer

know the other ways to insert the proteins in lipid bilayers Ram On Thu, Mar 4, 2010 at 4:36 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Gromacs Users, >> >> I would like to run molecular dynamics by inserting multiple proteins >> in the

[gmx-users] Multiprotein lipid bilayer

Dear Gromacs Users, I would like to run molecular dynamics by inserting multiple proteins in the same lipid bilayer using gromacs, is it possible? if so, please let me know if any tutorial is available or any kind of help is available Thanks in advance, Ram -- gmx-users mailing listgmx

Re: [gmx-users] grompp segmentation error

Dear Justin, I am having grompp segmentation error only for the drug-enzyme complex tutorial, all other executables are ok, can this occur due to the any other reasons like following the tutorial improperly. Thanks, Ram On Tue, Jan 5, 2010 at 1:24 PM, Justin A. Lemkul wrote: > > >

Re: [gmx-users] grompp segmentation error

Mon Aug 24 08:21:56 EDT 2009 compilers: C and fortran Intel 10.1 Please suggest me as the grompp command also donot work with this configuration. Thanks, Ram On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Th

Re: [gmx-users] grompp segmentation error

and help me. Thanks, Ram On Thu, Dec 31, 2009 at 11:49 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Gromacs Users, >> >> Iam following Drug/Enzyme complex solvation tutorial by John E. >> Kerrigan, I am unable to execute the grompp ste

[gmx-users] grompp segmentation error

Dear Gromacs Users, Iam following Drug/Enzyme complex solvation tutorial by John E. Kerrigan, I am unable to execute the grompp step as per the tutorial, the output of grompp command is as follows: grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr :

Re: [gmx-users] Truncation of file traj.trr failed

stin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> As per the suggestions in the bug, i changed the line in >> src/gmxlib/checkpoint.c file on the cluster: >> >> from >> outputfiles[i].offset = ( ((off_t) offset_high) <&l

Re: [gmx-users] Truncation of file traj.trr failed

(my mdp file is defined for 20 ns and the output is md20.tpr) or can i use the same tpr file (md20.tpr) or i require to change the command to continue.. Please help. Thanks, Ram On Fri, Nov 6, 2009 at 10:15 PM, ram bio wrote: > Dear Justin, > > Thanks for the information regard

Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin, Thanks for your patience and suggestions, as I am new to gromacs, i had to confirm my results. Ram On Mon, Oct 26, 2009 at 4:28 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> As per the suggestions, I have run NPT equil

Re: [gmx-users] Error during NVT equillibration with nvt.log file

SOL_CL- Thanks, Ram On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justion, >> >> When I executed the command g_energy -f anneal_npt1.edr, the output >> for temperature and pressure were as under: >> >> Sta

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

that can be the input for flexible docking. Thanks, Ram On Thu, Oct 22, 2009 at 4:59 PM, Mark Abraham wrote: > ram bio wrote: >> >> Dear Mark, >> >> You mean that I should consider a configuration with the lowest total >> energy for docking studies..Please c

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

Dear Mark, You mean that I should consider a configuration with the lowest total energy for docking studies..Please clarify and suggest me. Thanks, Ram On Thu, Oct 22, 2009 at 3:56 AM, Mark Abraham wrote: > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the sug

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

Dear Justin, Thanks for the advice, will try to follow using grace. Ram On Wed, Oct 21, 2009 at 8:25 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin. >> >> Thanks for the suggestion, definitely i would run next time for a >> longer tim

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

retrieve the lowest energy configuration is correct. Thanks, Ram On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the suggestion and advice. >> As i have used a modelled prote

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

wrote: > > > ram bio wrote: >> >> Dear Mark, >> >> Thanks for the advice and suggestions. >> >> I have used trjconv command as in the justin tutorial (trjconv -s >> md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact), >> but whe

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

, Ram On Wed, Oct 21, 2009 at 4:42 PM, Mark Abraham wrote: > ram bio wrote: >> >> Dear Gromacs Users, >> >> I have performed a protein in solvent simulation for 1 ns, the got the >> output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log >> m

[gmx-users] Protein Solvent Dynamics - Coordinates for docking

Dear Gromacs Users, I have performed a protein in solvent simulation for 1 ns, the got the output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log md_0_1.tpr md_0_1.trr md_0_1.xtc. I am following Justin Tutorial. Can anybody tell me how to extract the coordinates ? of the simulated prot

Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin, Thanks, will be back after some trials. Ram On Tue, Oct 20, 2009 at 8:16 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the advice and suggestions, will look into the plots and >> try to run a fur

Re: [gmx-users] Error during NVT equillibration with nvt.log file

orial, > equilibrating membrane systems takes a *long* time, anyway. > > -Justin > >> Regarding the gaps in the lipid bilayers,now when i visualized the >> .trr file in the VMD there were no gaps in the lipid bilayer, that is >> they did not move apart. >> >>

Re: [gmx-users] Error during NVT equillibration with nvt.log file

, 2009 at 7:40 PM, Justin A. Lemkul wrote: > > > ram bio wrote: > > > >> Now as i would like to proceed further, please suggest me how to >> confirm that the simulated annealing was proper and also please let me >> know can i now go to npt equillibration using the

Re: [gmx-users] Error during NVT equillibration with nvt.log file

: grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n index.ndx -o npt.tpr Thanks, Ram On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks and I tried your suggestion, that is

Re: [gmx-users] Error during NVT equillibration with nvt.log file

the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- please suggest me is it ok to remove the constraints and run the NVT equillibration. Thanks Ram On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul wrote: &g

[gmx-users] Error during NVT equillibration with nvt.log file

Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I

[gmx-users] Error during NVT equillibration

Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then, I

[gmx-users] Gromacs installation on the cluster

Dear Gromacs Users, About Gromacs installation on the cluster, we compiled it on both the login node and the computing nodes. I'd like to know which gromacs programs can be run on the login node without disturbing all other users and which ones must be run on the computing nodes (e.g. the MD progr

Re: [gmx-users] step 0Segmentation fault

ilayer. Thanks, Ram On Tue, Oct 6, 2009 at 5:39 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> As suggested, when i reexamined the system.gro (protein_newbox + >> dppc128) one of the ends of the problem (as i think) i.e. few &

Re: [gmx-users] step 0Segmentation fault

and position it in the bilayer and redo the inflategro procedure. Thanks Ram On Tue, Oct 6, 2009 at 4:42 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the advice. I am using the DPPC 128 lipid bilayer from D. >> Peter

Re: [gmx-users] step 0Segmentation fault

ed En.Temperature Pressure (bar) Cons. rmsd () 3.08099e+172.31982e+151.01551e+167.25066e+04 Please diagnose the information and suggest. Thanks ram On Tue, Oct 6, 2009 at 4:12 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Gromacs Users,

[gmx-users] step 0Segmentation fault

Dear Gromacs Users, I have inserted the protein in lipid bilayer and performed Inflategro I am able to reach the required area per lipid after certain iterations but was unable to get the standard Epot and Fmax values that is negative and to the power of 5 or 6 and Fmax less than 1000 during the l

Re: [gmx-users] 256 DPPC bilayer

Dear Justin, Thanks. Ram On Mon, Oct 5, 2009 at 7:30 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Gromacs Users, >> >> I am looking for a DPPC bilayer system of 256 and above , can anybody >> suugest me the site from where I can download P

[gmx-users] 256 DPPC bilayer

Dear Gromacs Users, I am looking for a DPPC bilayer system of 256 and above , can anybody suugest me the site from where I can download Please... Thanks Ram ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/

Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water

Dear Justin, Thanks for the suggestions and will be back after sometime after following the trials. Ram On Tue, Sep 29, 2009 at 10:45 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> I was trying to model a part of the protein involve

Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water

some proteins. Thanks Ram On Tue, Sep 29, 2009 at 10:16 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks and as per suggestion, now i have corrected the original >> modelled pdb file and executed the pdb2gmx command with

Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water

, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Dear Gromacs Users, >> >> Thanks Justin and Marc for the response and you were right. >> >> As suggested, i had a view in the modelled protein pdb file and here >> both the terimus are capped t

Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water

the total number of atoms in pdb file (4815) are not matching even though the number of residues are matching after pdb2gmx step. Thanks, Ram and selected choose the "Gromos96 53a6" parameter and "none" options On Tue, Sep 29, 2009 at 7:04 PM, Justin A. Lemkul wrote:

[gmx-users] neutralizing membrane protein in lipid bilayer +water

Dear Gromacs users, I have a modelled protein whose net charge is +12.69, and I would like to ionize the protein to make it neutral using genion command, but in genion command we can add a specific number of postive or negative charged ions which for my case would not completely neutralize the sys

Re: [gmx-users] nvt.gro

Dear Justin, Thanks for the options and suggestions, will be back after some trials with modelled proteins. Ram On Mon, Sep 28, 2009 at 6:17 PM, Justin A. Lemkul wrote: > > > ram bio wrote: > >> Dear Justin, >> >> When I used the energy mininized system f

Re: [gmx-users] nvt.gro

suggest, is it the right way i am following..as i will be not be using NVT equillibration anywhere through out the process. Thanks, Ram On Fri, Sep 25, 2009 at 11:23 PM, Justin A. Lemkul wrote: > > > ram bio wrote: > >> Dear Justin, >> >> As suggested, i increas

Re: [gmx-users] nvt.gro

suggest me what to do to lower the gap after NVT equillibration even after applying the lipid restraints and is it ok for my NPT equillibration as there are no gaps between the layers after this NPT equillibration. Thanks Ram On Tue, Sep 22, 2009 at 8:25 PM, ram bio wrote: > Dear Justin, > &g

Re: [gmx-users] nvt.gro

Dear Justin, Thanks for the suggestion, will try to apply position restraints on lipid as mentioned in the advanced trouble shooting section. Ram On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul wrote: > > > ram bio wrote: > >> Dear Gromacs Users, >> >> I am fo

[gmx-users] nvt.gro

Dear Gromacs Users, I am following the justin tutorial on KALP-15 in lipid bilayer, I have a query regarding the nvt.gro that is after the NVT equillibration phase. The mdrun was proper without any warnings or errors, but when i visuallized the nvt.gro in VMD, i found that the peptide is intact in

[gmx-users] Inflategro

Dear Gromacs Users, While I was runing the Justin's tutorial that is KALP-15 in DPPC , I have some queries regarding the INFLATEGRO, Please have patience to read and answer my queries: 1) does the system.gro should include the position restrained file of KALP_newbox.gro after running genrestr,