[gmx-users] Missing bond

Dear All, While I am preparing my system topology with pdb2gmx for a system containing enzyme with 30 non-ionic surfactant molecules in water, I got 36 number of bonds per surfactant molecules, but actually it has 37 bonds (anyways, the number of angle, dihedral etc. are correct). From the

[gmx-users] INTERPRETING THE ENERGY VALUES AFTER SIMULATIONS IN GROMACS

Hi gromacs users, After protein ligand simulations, I want to do energy analysis. How to interpret the following data properly? What books and papers should we refer? Energy AverageErr.Est. RMSDTot-Drift

Re: [gmx-users] gmx xpm2ps

Thank you very much From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Diogo Vila Viçosa Sent: Friday, March 31, 2017 5:00 PM To: gmx-us...@gromacs.org Subject: Re:

Re: [gmx-users] gmx xpm2ps

Thank you very much. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Friday, March 31, 2017 4:52 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users]

[gmx-users] HYDROGEN BOND EXISTENCE MAP

Hi gromacs users, In the perl script to calculate hydrogen bond %, the command is perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx What should the structure.pdb file contain? How to obtain it? At which point of simulations? Thanks, Neha -- Gromacs Users mailing list *

Re: [gmx-users] gmx xpm2ps

"gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red" -> "gmx xpm2ps -f hbmap.xpm -o hbplot.eps -rainbow red" You have a blanck space between the "-" and the "o". On Fri, Mar 31, 2017 at 5:52 PM Kulkarni R wrote: > Hi gromacs users, > > > After completing

Re: [gmx-users] gmx xpm2ps

On 3/31/17 11:27 AM, Kulkarni R wrote: Hi gromacs users, After completing production run, I gave this command gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red However, I got error, --- Program: gmx xpm2ps, VERSION 5.1.1 Source

Re: [gmx-users] Restraining Protein-ligand distance

> > On 3/27/17 8:42 AM, Juan Jos? Galano Frutos wrote: > > Hi there, > > > > I am trying AFEC simulations in complex (ligand-protein), but sometimes I > > get the ligands out the binding site, but I dont want that scenary. I was > > thinking the situation of applying distance retraints between a

[gmx-users] gmx xpm2ps

Hi gromacs users, After completing production run, I gave this command gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red However, I got error, --- Program: gmx xpm2ps, VERSION 5.1.1 Source file:

Re: [gmx-users] FAD parameters in CHRAMm36 ff

Thanks Dr. Justin for your reply On Fri, Mar 31, 2017 at 6:11 AM, Justin Lemkul wrote: > > > On 3/31/17 3:54 AM, Vytautas Rakeviius wrote: > >> I think you should use cgenff for FAD in such case. They are compatible >> and can by used together. >> >> > Indeed, though one should

Re: [gmx-users] Replica Exchange for surface tension

On 3/31/17 8:13 AM, gozde ergin wrote: Hi Justin, I found a new optimized NBFIX parameter for SOD-Oxygen of Betaine and SOD-Oxygen of SDS. On the other hand since betaine is a zwitterionic molecule there is + charge on Nitrogen(N) and - charge on the Oxygen atoms and SDS is anionic there is

Re: [gmx-users] Replica Exchange for surface tension

Hi Justin, I found a new optimized NBFIX parameter for SOD-Oxygen of Betaine and SOD-Oxygen of SDS. On the other hand since betaine is a zwitterionic molecule there is + charge on Nitrogen(N) and - charge on the Oxygen atoms and SDS is anionic there is - charge on SO4 and there is + SOD

Re: [gmx-users] Protein preparation

On 3/30/17 9:59 AM, Quin K wrote: Thank you. There are so many pdb structures for the protein I'm looking for. I'm not sure which one to pick. What should I look for when picking a protein pdb structure? I want to test for an inhibitor with the protein. Which of the following I should look

Re: [gmx-users] terminated abnormally, message of GridMAT-MD tool

On 3/29/17 10:10 PM, Мижээ Батсайхан wrote: Dear Justin, I am using GridMAT-MD tool for analyses of heterogeneous membranes. I generated trajectory.gro only a group which contains a peptide and lipids. I got following Thread 1 terminated abnormally: Illegal division by zero at

Re: [gmx-users] vsites with CHARMM force fields

On 31 Mar 2017, at 10:51, Ramon Crehuet Simon > wrote: In that case, does it make sense to use virtual sites to allow 4fs time step? In other words, if vsites remove the fastest degrees of freedom, but we do not constrain bond

[gmx-users] equilibration and production run

Hi gromacs users, I intend to do the following steps for protein ligand simulations (for linear interaction energy) (1) Energy minimization (2) NVT equilibration (with restraints on protein and ligand) (3) NPT equilibration (with restraints on protein and ligand) (4) NPT production During NVT

Re: [gmx-users] FAD parameters in CHRAMm36 ff

I think you should use cgenff for FAD in such case. They are compatible and can by used together. On Friday, March 31, 2017 9:29 AM, Amir Zeb wrote: Hello Folks, I want to simulate a protein where FAD is included as co-factor. I will use CHARMm36 ff but I don't

[gmx-users] vsites with CHARMM force fields

Dear all, I am simulating a system with CHARMM36m force field. Following the recommendations in the mailing list and the gromacs web page, I constrained only h-bonds (constraints = h-bonds). In that case, does it make sense to use virtual sites to allow 4fs time step? In other words, if

[gmx-users] analysis of osmolyte at particular distance from backbone

Dear all, I want to calculate the number of osmolyte molecule at particular distance from backbone with respect to residue.I have tried the command trjorder but it gives the number of osmolytes w.r.t time and i want it w.r.t residue. Can anyone help me how to calculate this. Thanks in advance --

Re: [gmx-users] Pdb2gmx

Dear Lamm, It is GROMACS-5.0.7. So you need to use "gmx pdb2gmx" command. Best Wishes, Saumyak On 31 March 2017 at 11:55, Lamm Gro wrote: > Dear Gromacs users , > > I have installed Gromacs by this way : > http://www.gromacs.org/Documentation/Installation_ >

[gmx-users] calculating gbsa parameters for metal ion

Hello and greetingsi am simulating my protein in implicit solvent. the protein has ca2+ ion in it. the gbsa.itp file doesn't have parameters for any ion.how can i add parameters of my ion?As mentioned in tutorial.[ implicit_genborn_params ];Atomtype sar st pi gbr hct Values in columns 1-3

[gmx-users] FAD parameters in CHRAMm36 ff

Hello Folks, I want to simulate a protein where FAD is included as co-factor. I will use CHARMm36 ff but I don't know the residue ID for FAD in this particular forcefield. Anyone please let me know by which name FAD is represented in CHARMm36 ff? Thanks in advance! ~Amir -- Gromacs Users

[gmx-users] Pdb2gmx

Dear Gromacs users , I have installed Gromacs by this way : http://www.gromacs.org/Documentation/Installation_Instructions_5.0#quick-and-dirty-installation every thing was fine and I could install the package completely . But now I can't find pdb2gmx command ! Can you please let me know what

Re: [gmx-users] MMPBSA analysis on GROMACS trajectory

Thank you for the reply. I am using cygwin64 for my computations. Had already tried the above mentioned link. It is not working in CYGWIN64. Thanks, Neha On Mon, Mar 27, 2017 at 1:07 PM, masoud keramati wrote: > Hi > They have a web site and all of things you