Re: [gmx-users] overriding -ignh flag

Sir i am using gromos54a7 ff -- * with regards* *Yogesh Sharma* -- 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

[gmx-users] overriding -ignh flag

hi everyone, I want to override -ignh tag as this tag is stripping hydrogens off amino acid side chains, which might incorporate artifacts. my N and C terminals are NH3+ and coo- gmx pdb2gmx -f y.pdb -o y_pro.gro -water spc -his -ter i am getting Fatal error: Atom HA in residue MET 1 was not

Re: [gmx-users] Protein pore collapse during simulation.

sir, in efforts to find out the differences in the density of bilayers generated by charmm and gromac(berger lipids) i used grid-mat. there are significant differences in area per lipid. with these settings for both systems: override_vectors5.2,10.0,6.9 grid20

[gmx-users] Customize gromac FF for lipid parameters

want to run simulations in charmmff -- * with regards* *Yogesh Sharma* -- 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

Re: [gmx-users] choice of ?Qm Optimized Energy

://atb.uq.edu.au/molecule.py?molid=364968 *with regards* *Yogesh Sharma* -- 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

[gmx-users] choice of ΔQm Optimized Energy

Greetings everyone, I was looking at the parameter files of a ligand. I found four files of ligand under the same name but differences were there in ΔQm Optimized Energy -1556371.3071 kJ.mol-1 -0.525 0.429 -0.250 which one should I use for my ligand interaction studies? looking forward for your

Re: [gmx-users] Protein pore collapse during simulation.

membrane protein with a ligand. whose parameters are only available in gromacff (ATB). #ligand contain metalloid atoms. *with regards* *Yogesh Sharma* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Protein pore collapse during simulation.

Hi I have used inflategro to pack protein in lipid bilayer. While simulation run protein channel is getting collapsed. can i get some suggestions, if it is because of the wrong orientation of my protein in bilayer or lesser area per lipid after shrinking iterations? i have used charmm assembly as

Re: [gmx-users] charmm gui pdb to gro

*thanks sahil * *but i am interested in lipid molecule conversion not protein. I think pdb2gmx will work for protein molecules only.* -- 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

[gmx-users] charmm gui pdb to gro.

Greetings, hey, I want to convert the charmm gui generated pdb (membrane + protein) to gromacs readable file. charmm generated lipids contain hydrogen atoms and naming differences. I tried doing it manually but couldnt succeed. Is there any script available for atom renaming and reordering? I

[gmx-users] system has non zero net charge

Greetings, I am performing membrane protein simulation in the presence of a biomolecule. topology for the molecule was downloaded from ATB server. After simulation run, I found unexpected behviour of the added biomolecule. This ligand named UINL was showing affinity to ASP and GLU residues.

[gmx-users] molecule breakage during minimization

Hello everyone, Before equillibriation I was trying to minimize my protein membrane system. energyminimized.gro file when vizualized in vmd showed few lipid molecules broken. Is it safe to use trjconv to make whole molecule after em or i can proceed with breakage? This is the minimization.mdp

Re: [gmx-users] g_membed mdp file

Sir, I tried using inflategro but bash script is not compatible with my version i guess. I am getting error ## RUNNING SHRINKING ITERATION {1..26}...#run_inflategro.sh: 32: run_inflategro.sh: Illegal number:

[gmx-users] g_membed mdp file

Hello users If someone is working on membrane protein. I am looking for sample mdp file for g_membed compatible with gromacs5. I used mdps available in original references (http://wwwuser.gwdg.de/~ggroenh/membed.html) but those seems to be totally outdated. *with regards* *Yogesh Sharma

Re: [gmx-users] Overriding atom type.

greetings Dr. Justin I used charmm gui Input generator for ligands. these are H2O2, NO and Urea. I got three files for each Charmm36.itp, ligand.itp and topol. top. I added charmm36.itp files for each ligand under subsequent section with my system.itp and added #include link for ligand.itp

Re: [gmx-users] Overriding atom type.

Thank you Dr. Alessandra I actually generated topologies for my ligands using charmm server generated itp files had few overriding names, which are throwing errors when combined. Please have a look at the itp files pasted here.

[gmx-users] Overriding atom type.

1 1.0080 0.500 A4.00013524445e-02 1.924640e-01 OG311 815.9994 -0.500 A3.14487247504e-01 8.037464e-01 * thank you for your precious time.* * with regards* *Yogesh Sharma* -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] segmentation fault core dumped

738 I am attaching picture here for 4411 atom containing residues for reference. Both of the atoms are inside box parameters. I even decreased temperature to 1K or 30K but all in vain Can you help me with this? Thank you. * with regards* *Yogesh Sharma* -- Gromacs Users mailing l

[gmx-users] (no subject)

738 I am attaching picture here for 4411 atom containing residues for reference. Both of the atoms are inside box parameters. I even decreased temperature to 1K or 30K but all in vain Can you help me with this? Thank you. * with regards* *Yogesh Sharma* -- Gromacs Users mailing list * Ple

Re: [gmx-users] ligand topology building.

. * with regards* *Yogesh Sharma* -- 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

[gmx-users] ligand topology building

hello users I am using ATB server for ligand topology development. there is a section named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP what does it mean? and in files section there is choice for Topology Files and structure files as following GROMACS G54A7FF All-Atom (ITP

Re: [gmx-users] setting up osmotic gradient across bilayer.

Thank you Dr. Dallas But my concern is setting water concentration difference in exterior and interior of cell membrane not box size adjustment. Is there any way or some scripts available to do so? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] setting up osmotic gradient across bilayer.

Hello users I am trying to check water transport through a membrane protein. I ran simulation for 10 ns. In first attempt I couldn't see significant transport through protein although pore was filled. I hypothesized it could be due to osmotic equilibrium. so in my next mdrun I deleted all water

[gmx-users] Concentration gradient across bilayer

hello guys, I want to monitor water transport across my membrane protein. i ran simulation of 10 ns but i didnt set up water concentration gradient across bilayer. Will my protein show water permeability without gradient if, its passive transport. Can anyone suggest me a way to develop

[gmx-users] INFLATEGRO SHRINKING SCRIPT ERROR

hello everyone, I have been struggling with the automated script for shrinking iteration in Professor lemkul tutorials. can anyone spot what am I doing wrong here? * sh

[gmx-users] increase number of lipids in 128popc.pdb

hello guys, I downloaded 128dppc.pdb file from calgary uni website bilayer but charmm gui area calculator showed to use atleast 180 residues in upper and lower leaflet. how can I increase lipid number; avoiding atomic clashes ? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] charmm36M generated topology conversion to GROMOS54A7 ff

hi users, I generated ligand topology containing complex metals using ATB server, developed using GROMOS54A7 modified forcefield. Then i used Charmm gui for protein embedding in lipid bilayer followed by catenation of both .gro files. System was solvated but during ion addition it couldnot

[gmx-users] Running iteration for lipid shrinking using InflateGRO methodology

hello users, I am using inflategro methodology to pack lipids around membrane protein. I used bash script for iteration cycle provided by Justin Lemkul *. * But unexpectedly, cycle is dying here *gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o tmp.gro

[gmx-users] Atom type 'AS' not currently supported by GROMOS.

i want to simulate arsenic containing molecule in gromacs. i tried to develop topology of the molecule but I am getting error "Atom type 'AS' not currently supported by GROMOS". Is gromacs restricted to use some metals like Arsenic? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] CHARMM GUI membrane builder's assembled output

Greetings, I used charmm gui's custom Membrane/protein builder to assemble components for MD simulation. It gave me equillibriated box. I am confused whether I should equllibriate box again or not? From which step should I start in Gromac,Energy minimization, equillibriation or Production MD? --

[gmx-users] ADDITION OF COMPLEX IONS OUTSIDE BILAYER FOR TRANSPORTER PROTEIN SIMULATION

?and what are important parameters that i need to keep in mind during simulation. like specific modifications of the program? * with regards* *Yogesh Sharma* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] query:

?and what are important parameters that i need to keepin mind durring simulation. like specific modifications of the program? * with regards* *Yogesh Sharma* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting