[gmx-users] Invalid order for directive defaults

Dear Justin Thanks for your quick reply. I was confused. If I add #include "ffcntbon.itp" after #include "cnt.itp" in .top file, my problem was solved and error was solved? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the

[gmx-users] Invalid order for directive defaults

Dear Justin Thanks for your reply. > In your previous setup, you were effectively trying to use CHARMM27 + some > other > force field related to the CNT. You can't do that. Thus, Gromacs is not appropriate for systems containing cnt. Is my deduction true? In my case, peptid + cnt + water mole

[gmx-users] Invalid order for directive defaults

Dear Justin My cnt is infinite. I obtained cnt.top by g_x2top and then modified cnt.top to cnt.itp. For obtaining cnt.top, I used following files: --- ffcnt.atp: CA 12.01100 ; aromatic C --

[gmx-users] Invalid order for directive defaults

Dear Justin Very thanks for your reply. I created a new topol.top file as below: 1) I used once default directive. 2) I put cnt.itp file in working directory. 3) I copied pr.top and renamed it to topol.top. I added #include "cnt.itp" in the end of topol.top file. I modified [ molecules ] direc

[gmx-users] Invalid order for directive defaults

Dear all My system contains protein + cnt + water molecules. I have summarized what I did below: --- 1) By pdb2gmx and charmm27 force field, I obtained pr.top for protein then I converted it into pr.itp by deleting

[gmx-users] time evaluation of dimensions of the simulation cell

Dear gromacs usres I am doing simulation of lipid bilayer. I did 2 steps: 1) energy minimization, 2) equilibration. Before production run, I want to monitor dimensions of the simulation cell to test the stability of the simulation. On the other hands, I want to plot dimensions of the simulation

[gmx-users] emstep unit

Dear Justin Thanks for your reply. Ok. You are right. There is no "time" during EM. For example, if I use nstep = 10,000 and emstep = 0.01, what means of Step size in this case, exactly? Please give me more explanation. Best wishes for you. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] emstep unit

Dear gromacs users What is the reason of this point that unit of the emstep (step size)is nm? I think ps (unit of time) is more resonable. If I am wrong, please give me explanation about this point. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] fftw

Dear gromacs users Why should I install fftw before gromacs installation? I want to know exact role of fftw in gromacs calculations. Please guide me about that. Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search t

[gmx-users] LAMBADA and InflateGRO2

Dear gromacs users I want to use LAMBADA and InflateGRO2 to create a system containing dopc lipid + cholesterol + drug. When I use ~/lib/lambada/lambada_rc1/lambada -f1 drug.gro -f2 lipid_chol.gro I encountered with Illegal division by zero at /home/karami/lib/lambada/ lambada_rc1/lambada line

[gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

Dear Baptiste Very thanks for your reply. Unfortunately, I have not access to InflateGro2. I encountered with error. If there are a script for InflateGro2 like InflateGro. please sent me perl script related to InflateGro2. Best wishes. -- gmx-users mailing listgmx-users@gromacs.org http:/

[gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

Dear Justin Thanks for your quick reply. I want to study a system containing DOPC and cholesterol and drug. I correctly prepared gro files and topology parameters for this system. I did previous step (Step Two: Modify the Topology) without problem. I have 2 problems. 1) After I use trjconv -

[gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

Dear Justin I do your tutorial entitled " KALP15 in DPPC ". In Step Three: Defining the Unit Cell & Adding Solvent, You said "Use trjconv to remove periodicity ". When I use trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact, gromacs tell me: Select group for output. Wh

[gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus

Hi all. After using amber03 force field for protein-ligand simulation (pdb2gmx), I encountered with following error: Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus. Ligand in my system is a single residue (GLN). There are [GLN], [NGLN] and [CGLN]

[gmx-users] RMS fluctuations and error estimate from block averaging

Dear all I have a question about g_analysis with option -ee. What is difference between RMS fluctuations and error estimate obtained from block averaging? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

[gmx-users] g_dist without output file

Dear Lina Very thanks for your time and attention. Initial command was : g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5 After running following command the problem was solved : g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 5 t: 17008 6773 NA 21881 NA 3.05534 (nm) t: 17008 677

[gmx-users] g_dist without output file

Dear Lina There is not any things related to list of atoms on the terminal. Best regards -- 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! Pleas

[gmx-users] g_dist without output file

Dear Lina Thanks for your reply. Without the -dist 0.5, I get the -o dist.xvg output, but I need list of the all atoms in group 2 closer than dist to the center of mass of group 1. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please searc

[gmx-users] g_spatial (gromacs 4.5 manual)

Dear gromacs users I read g_spatial tool of gromacs 4.5 manual. I have many questions. There are in the manual: USAGE: 1. Use make ndx to create a group containing the atoms around which you want the SDF 2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none 3. trjconv -s a.tpr

[gmx-users] g_dist without output file

Dear all When I use g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5, program was done without error, but it don't create output file (dist.xvg) in the directory in which g_dist tool was run. What is reason of this case? Any help will highly appreciated. -- gmx-users mailing listgm

[gmx-users] position restrained minimization on the one part of a system

Dear Justin thanks for your attention I deleted posre.itp file which pdb2gmx was created (containing all solute).I made a posre.itp (containing only protein) by genrestr. now if I use define = -DPOSRES, gromacs use from my posre.itp. is it true? -- gmx-users mailing listgmx-users@gromacs.or

[gmx-users] position restrained minimization on the one part of a system

I want to use define = -DPOSRES_Protein_chain_A for step 1. is it true? -- 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

[gmx-users] position restrained minimization on the one part of a system

Dear Mark thanks for your reply you said "if pdb2gmx is able to treat the whole system in one pass, then it will write such position restraint files automatically" in my system, what pdb2gmx includes are in below: ; Include forcefield parameters #include "amber03.ff/forcefield.itp" ; Include c

[gmx-users] position restrained minimization on the one part of a system

Dear all my system contains protein + ligand+ water molecules. protein + ligand = solute water molecules = solvent I want to do minimization energy in 3 steps : step 1) on protein only step 2) on all solute (protein + ligand) step 3) on all system should I use position restrained minimizati

[gmx-users] distance and angle cutoff for hydrogen bond

Dear gromacs users in gromacs manual, there is [-a real 30 Cutoff angle (degrees, Acceptor - Donor - Hydrogen) -r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)] I think that in hb (D-H...A) distance of 0.35 nm = distance between D and A. and angle of 30 = acceptor-donor–hydrogen an

[gmx-users] .psf and .dcd files

Dear Ran thanks for your reply. Is psfgen a separately program? -- 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

[gmx-users] .psf and .dcd files

Dear gromacs users I did simulation of protein-ligand by gromacs 4.0.7 with amber 03 forcefield. I need to .psf and .dcd files. can I convert/obtain them? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

[gmx-users] water molecules (interfacial)

Dear Justin I used g_dist -f .xtc -s .tpr -n .ndx -o -lt -dist 1 but program give me only lifetime.xvg. there are no dist.xvg file. why? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Sup

[gmx-users] water molecules (interfacial)

Dear Justin are you sure g_dist -dist give me what I need. if so, how? since, dist.xvg gives distance vs time and lifetime.xvg gives number of contact vs time. while, I want number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation.

[gmx-users] water molecules (interfacial)

Dear Mark and gromacs users thanks for your time and attention. how to make selection.dat file? what should be in that? please clarify this new tool more. how can I obtain what I need (number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand durin

[gmx-users] water molecules (interfacial)

Dear all my system includes protein, ligand and water. I want to obtain number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand. -- gmx-users m

[gmx-users] y-axis label in hbang and hbdist.xvg file

Dear Justin count = count of hydrogen bonds being in a certain distance (between 0-0.35) and angle (between 0-30)? -- 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/Sear

[gmx-users] y-axis label in hbang and hbdist.xvg file

Dear Justin very thanks for your attention. I have another question about g_hbond. in manual, -dist and -ang are distance and angle distribution of all hydrogen bonds respectively. I want to know in hbang and hbdist.xvg file, what is y-axis label? -- gmx-users mailing listgmx-users@gromacs.

[gmx-users] -don (g-hbond)

Dear Justin I confused. number of donors in donor.xvg file is 203. while, when use g_hbond: found 143 donors. Select a group: 2 Selected 2: 'Protein_A' Select a group: 3 Selected 3: 'Protein_B' Checking for overlap in atoms between Protein_A and Protein_B Calculating hydrogen bonds between Prote

[gmx-users] -don (g-hbond)

Hi all I want to know regarding 2nd and 3rd column of donor.xvg output about g_hbond -don. -- 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! Pleas

[gmx-users] -don (g-hbond)

Dear Justin Header of file is as follow: @title "Donor properties" @xaxis label "Time (ps)" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Nbound" @ s1

[gmx-users] -b -e

Dear gromacs users my simulation time is 10 ns (1 ps), but, I want to use last 4ns for analysis. for example, if I use g_rms -b 6000 -e 1 -o rmsd.xvg, in xvg output file, rmsd plotted versus time (from 6000 to 1 ps in horizontal axis). while I want horizontal axis be from 0 to 4000 ps

[gmx-users] trjconv -pbc

Hi gmx users Perhaps, this question be repetitive. I want to know using trjconv -pbc is only a solution for visualization problem? Is there feasibility to use old trajectory file (with out trjconv -pbc) for any kind of analysis without any problem? -- Atila Petrosian Ph.D. student of BioPhysical

[gmx-users] residence time of water molecule and life time of hydrogen

*Dear Justin* ** *I read manual and specially g_hbond. but manual doesn't gime me information about * residence time of water molecule and life time of hydrogen. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] residence time of water molecule and life time of hydrogen

Hi gromacs users I am beginner in gromacs. I did md simulation of a protein by gromacs and now I want to obtain residence time of water molecule and life time of hydrogen bonds. Can I obtain both of them using gromacs? please guide me by detail. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] contact map

Hi gromacs users after simulation of protein-ligand, in analysis section, how to obtain contact map for protein-ligand? thanks in advance. -- atila -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gro

[gmx-users] residence time of water molecule

Hi how to obtain residence time of water molecule using md simulation and gromacs? What is the best way to do this? Please suggest. -- atila -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org