[gmx-users] Fatal error

Hi Gromacs user, I changed the version and this time it gave the following error s...@linux-g1cj:~/Desktop/283> g_energy -f md283.edr -o md283-TE.xvg :-)  G  R  O  M  A  C  S  (-: Gnomes, ROck Monsters And Chili Sauce     :-) 

[gmx-users] Fatal error

Hi gromacs users, the other fatal error which is produces from my last year data is: s...@linux-g1cj:~/Desktop/283> g_rms -s em.tpr -f md283.trr -o md283-rmsd.xvg :-)  G  R  O  M  A  C  S  (-:    GROningen MAchine for Chemical Simulation  

[gmx-users] analysis eror

Hi gromacs users. I need help with the old data generated by gromacs. It is about a year older. I used the command and the output is: s...@linux-g1cj:~/Desktop/283> g_energy -f md283.edr -o 283te.xvg :-)  G  R  O  M  A  C  S  (-:    Good gRace! Old Maple

[gmx-users] Input output file error

Hi Gromacs Users, I used gromacs in 2007 and have data of that and now want to used that data by making graphs but the following errors occured: 1) Input output file error. 2) Fatal error. version 40 with version 20 program. I think I used some version of gromacs 3.0.3 or other at that

[gmx-users] Frames problem

Hi All, I have MD simulation which crashed and I combine the frames with trjconv. Now the problem is that when I do analysis like that of Solvent accessible surface area, it showed that the incomplete frame . I use the gmxcheck with the following result d 1: 'Protein' 1695 out of 2854 atoms were

[gmx-users] secondary structure

Hi All, I want to study and calculate the secondary structure as a function of time of my MD simulated protein. I have no DSSP installed but will use VMD for this.Can any one suggest me which files of MD simulation output I should used? or I need to develop PDB file of the whole MD simulation tr

[gmx-users] Help for GNUPlot

Dear Mark, Hi ! Currently I tried to install xmgrace but the toolbar menue is not shown on window screen so I am using gnuplot for analysis as I have little know how about unix/linux.Please set to me the following. [EMAIL PROTECTED]:~> cd project [EMAIL PROTECTED]:~/project> ls #bfac.pdb.1# con

[gmx-users] Alternate to xmgrace

Dear Mark, Hi ! Is there any alternate software to xmgrace, which I can use for my MD simulation results and which is compatible with gromacs? As I have installed xmgrace in my computers but the xmgrace window icons and tool bar is not shown properly. Regards, Lal badshah Send instant messag

[gmx-users] Can not open file:md323.xtc

Hi All, During analysis the following error also came; [EMAIL PROTECTED]:~/project> g_rmsf -s md323.tpr -f md323.xtc -o rmsf.xvg -oq bfac.pdb :-) G R O M A C S (-: Giant Rising Ordinary Mutants for A Clerical Setup :-)

[gmx-users] Error of g_rms

Hi All, I am analysing my results of simulation of protein, the following error comes, I don't know about the reason.Please guide me. Program g_rms, VERSION 3.3.1 Source code file: smalloc.c, line: 113 Fatal error: calloc for atomtypes->radius (nelem=2028871473, elsize=4, file tpxio.c, line 1017

[gmx-users] Error of mdrun

Dear Mark, When I enter from root account the following is the result: linux:~ # which mdrun /sbin/mdrun linux:~ # which grompp /usr/bin/grompp linux:~ # But from user account the which mdrun usr/bin/mdrun and also the which grompp /usr/bin/grompp occured. Actually I have very little experi

[gmx-users] Error of mdrun

Dear Experts, Hi ! I am doing MD simulation on two computer, on one when I want to start the EM and do the mdrun command the following error results: linux:~/project # mdrun -v -s em.tpr -c em.pdb mdadm: /dev/md-v not identified in config file. linux:~/project # mdrun -v -deffnm em mdadm: option

[gmx-users] GTP in topology

Hi All, I have taken the GTP topology from PRODRG server but now how can I make a connection with my original topology file: As in Errors of Gromacs it is mentioned ==> find a topology file for the residue / molecule and include as a .itp file, what does it means? I am using OPLS/aa force field

[gmx-users] Error in topology file

Dear Experts, Hi ! I am doing simulation of cholera toxin, one with GTP( guanosine triphosphate) and other without it.The without GTP MD simulation I have done, now I started the other and when I used the pdb2gmx command on pdb file it says: Program pdb2gmx, VERSION 3.3.1 Source code file: resall

[gmx-users] error for runing second simulation using the topology file

Dear Experts, Hi ! I am simulating a protein of about 185 residues.I did MD production of it of 500,000 nsteps at temperature of 310k. Now I want to simulate it at 283k I used the same topology and gro file already used for the first mentioned temp.But when I used these and give the command

[gmx-users] Simulation at different temperature

Dear Experts, Hi ! I want to simulate a protein at 298K, 283K, and at 323k.For all these temperature will I prepare different md.mdp files or single ? Regards, Lal badshah. Send instant messages to your online friends http://uk.messenger.yahoo.com __

[gmx-users] Command for MD

Dear Experts, Hi, I have done equilibration of a protein but during equilibration due to power supply cut off a crash occurred after which I restarted with the command tpbconv. Now I want to start molecular dynamics simulation but confused how to start them.My files before crash are: Pr.mdp

[gmx-users] Error in equilibration

Dear Justin, I try again by correcting the typo mistake I made, this time it gives the following type of out put; Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 224.227448 (between atoms 1932 and 1934) rms 4.182895 bonds that rotated more than 30 degrees: atom

[gmx-users] System

Dear Justin, Hi, I want to do MD simulation of cholera toxin A-subunit.I took PDB file and remove other complexes from the protein so it comes to 185 amino acid residues.Through Whatif server I added the missing atoms. I uses oplsaa force field.Added about 11700 water molecules, closed it in cub

[gmx-users] error oxo

Dear experts, Hi! I see the following on the site: Error 0x0 and 0x1 From FaHWiki Jump to: navigation, search The 0x0 and 0x1 errors are unknown errors - all errors that are known will end with some other error code and message, but those errors that Pande Group hasn't

[gmx-users] Error in equilibration

Dear Justin & Mark, Hi! I made changes in my pr.mdp file but still the errors came.Please guide me. title = pr.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 nsteps = 10 nstcomm =

[gmx-users] LINCS problem

Dear Experts, I checked the error lincs page and from that what I ignored in my work are the two errors these are: Warning: there are 0 atoms with zero occupancy and 1 atom with occupancy unequal to one (out of 1480 atoms).Check your pdb file Warning: masses will be determined based on residu

[gmx-users] pr.mdp file

Dear Justin and Mark, My pr.mdp file is: title = pr.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 nsteps =10 nstcomm = 1 nstxout = 250 nstvout = 1000 nstlog

[gmx-users] error of equilibration

Dear Justin & Mark, Hi ! I am doing equilibration and again the error comes with the following warnings in the pr.log file, Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 224.227219 (between atoms 1932 and 1934) rms 4.182889 bonds that rotated more than 30 degre

[gmx-users] complete energy minimization

Dear experts, Hi! I minimized the system and gies 10,000 nsteps, but the output is: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.9742134e+21 Maximum force = 4.1648520e+06 on atom 1934 Norm of force = 5.6

[gmx-users] ions different

Dear experts, I have done upto minimization but faults in equilibration I am again starting the minimization, now in adding ions of sodium the following error is given, what is the reason for this. Warning: atom names in topol.top and ions.pdb don't match (NA - Na) Warning: atom names in topol.to

[gmx-users] equilibration

Dear gromacs experts, I have decrease the timesteps from 50,000 to 10,000 but still the error of LINCS comes.where should I do correction? regards, Lal badshah/ SYED LAL BADSHAH M.Phil Scholar NCE in Physical Chemistry, University of Peshawar. NWFP,Pakistan. Cell # 03349060632. Send instan

[gmx-users] equilibration

Dear experts, Hi,I am doing equilibration ,it crashes a few times due to power breakdown.Now I started again witj the following commands and the following output comes.what should i do? please guide me grompp -f eq.mdp -c em.pdb -p topol.top -o eq.tpr nohup mdrun -s eq.tpr -o eq.trr-c eq_b4md.gr

[gmx-users] traj.trr

Dear gromacs users, Hi, In my simulation directory one file is present on the name of traj.trr Is this shows that my mdrun crashed? regards, SYED LAL BADSHAH M.Phil Scholar NCE in Physical Chemistry, University of Peshawar. NWFP,Pakistan. Cell # 03349060632. Send instant messages to your

[gmx-users] results of energy minimization

Dear gromacs experts, I have run the energy minimization of a protein.With the tail command it shows the following results: [EMAIL PROTECTED]:~/protein> tail -15 md.log NS-Pairs 94.365846 1981.68276620.0 Reset In Box 0.5693855.124465

[gmx-users] Error of atomtype not found

Dear Gromacs Users, The file which I used for ions.itp is, now I change oplsa_405 by Na but it give again the error Fatal error: Atomtype 'Na' not found! Please guide me. [moleculetype] ; Name nrexcl sodium 1 [ atoms ] ; nrtyperesnr residue atom

[gmx-users] Error of atomtype before minimization

Dear Gromacs Users, Hi! I have tried to correct my file before minimization by adding sodium ions but it gives error by showing no such molecule type,now I made the file of ions.itp through Unix editor.I follow the gromacs mail archive.After running the gmpp comand it gives the error: Fatal erro

[gmx-users] Error of moleculetype

Dear gromacs users, Hi, I have encounter the following error,after addition of Sodium ions to my system as it has -5.0 charge and before minimization. Fatal error: No such moleculetype Na I have checked errors of gromacs but I didn't understand that.Is I will write the word NA below the [mol

[gmx-users] Checking the Progress of Energy minimization

Dear All, I am doing Energy minimization of a protein.The valus are fluctuating butI don't know in how much time it will be completed and what are the signs that show that it is running? top - 09:54:08 up 22:52, 2 users, load average: 0.07, 0.17, 0.16 Tasks: 111 total, 1 running, 109 sleepin

[gmx-users] number of coordinates in coordinate file

Dear all, I am trying to do Energy Minimization of a protein.But it gives the following error: ERROR: invalid enum 'cut-��off' for variable vdw-type, using 'Cut-off' Next time use one of: 'Cut-off' 'Switch' 'Shift' 'User' 'Encad-shift' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# chec

[gmx-users] error in coordinate file

Hi, I am new to GROMACS.Currently I am working on a protein.For minimization I prepare file and when I gave the command in the shell the following output comes: Fatal error: number of coordinates in coordinate file (2a5f_b4ion.pdb, 40183) does not match topology (2a5f.top, 40612) Ple

[gmx-users] Loss of GTP in topology file.

Hi, I have added missing atoms to my pdb file through servers of WHATIF,when I use the force field option then the following output comes in shell console: Fatal error: Residue 'GTP' not found in residue topology database and the following files are created: 2a5f.top 2a5f_A.itp 2a5f_B.itp posr

[gmx-users] adding atoms in PDB file

Hi all, I am new to gromacs andI want to add atoms to pdb file , what is the method for this? Regrads, SYED LAL BADSHAH M.Phil Scholar NCE in Physical Chemistry, University of Peshawar. NWFP,Pakistan. Cell # 03349060632. Send instant messages to your online friends http://uk.messenger.yaho