[gmx-users] No ./configure file

I was trying to download grimaces. But it says, "No such file or directory" I tried make, but that too gave an error. It said, "No targets specified and no make file found". I tried installing version 5.1, 5.0 and 4.6. However, the same error persists. Please help! -- Regards, Raag -- Gromacs Us

[gmx-users] Fatal error: Residue 'GTP' not found in residue topology database"

Hi! I was trying to simulate tubular (1TUB.pdb). I could run the pdb.gmx step. I added the water molecules. But when I defined the force field (I chose 15), it gave an error. It said, " Fatal error: Residue 'GTP' not found in residue topology database" Please guide! -- Regards, Raag -- Gro

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 136, Issue 133

> Today's Topics: > >1. Re: Comparing various MD packages (Mark Abraham) >2. Re: Probable bug in 5.0.4 gmx enemat (Mark Abraham) >3. Re: Probable bug in 5.0.4 gmx enemat (Mark Abraham) >4. Fatal error: Residue 'GTP' not found in residue

[gmx-users] unable to plot graph using xmgrace

Hi! I tried plotting the potential energy of my molecule using xmgrace. But it gave a warning: Warning: locale not supported by Xlib, locale set to C Xmgrace opened but I could see no plot. I am new to computational biology. I am using gromacs on a mac.Can you please guide as to how I should

[gmx-users] mutating the protein

Hi! Gromacs is a beautiful software! I have been able to understand the dynamics of this protein I was trying to study. I wanted to see how the various amino acids could affect its dynamics. So I wanted to mutate the protein by replacing one particular amino acid by another one. How may I do tha

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 154

ves the pdb as 333leu.pdb. > > Best, > > > -- > Dr. Matej Repic > Ecole Polytechnique F?d?rale de Lausanne > Laboratory of Computational Chemistry and Biochemistry > SB - ISIC ? LCBC > BCH 4108 > CH - 1015 Lausanne > ---

[gmx-users] colleague subscribed to gromacs mailing list but unable to get replies

Hi! A colleague of mine is having a little problem with the gromacs mailing list. She says she subscribed to it, but when she posts, she gets no reply. She does get the digest, however. She asked me to ask you if you could kindly help her. -- Regards, Raag -- Gromacs Users mailing list * Plea

[gmx-users] free energy of mutated protein

Hi! I wanted to see the effect of mutations on a protein. So I mutated the protein using chimera and then calculated the potential energy and all using Gromacs. Is there a command, after the energy equilibration step, that I can use to find the free energy? -- Regards, Raag -- Gromacs Users ma

[gmx-users] generation of ions additional to solvent molecules

command I used was: genion -s ions.tpr -o PDB_solv_ions.gro -p topol.top -pname K -nname CL -np 84300 Is there a way to add ions additional to the solvent molecules, instead of replacing them? Thank you and regards, Raag Saluja -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] Gibbs' free energy in MD

Hi! How can I calculate Gibbs' free energy from the potential energy values obtained from the MD simulation? Regards, Raag -- 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.gro

[gmx-users] gibbs' free energy tutorial: help with write_mdp.pl

error at write_mdp.pl line 4, near "*\expandedcolortbl" syntax error at write_mdp.pl line 4, near "cssrgb\" syntax error at write_mdp.pl line 5, near "paperw11900\" "use" not allowed in expression at write_mdp.pl line 12, at end of line syntax error a

[gmx-users] gibbs free energy calculation

Hi! Thank you for your previous reply. You were right, my file was getting modified. I had not saved the page directly but had copy-pasted it in a textedit file. I am again stuck, though. I was trying to run job_0.sh and when I gave the command: gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE

[gmx-users] gibbs calculation: job.sh

Hi! When I give the command: perl write_sh.pl job.sh I get this error: readline() on closed filehandle IN at write_sh.pl line 19. Can you please help out? Thank you in advance! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Us

[gmx-users] gibbs calculation

Hi! I was calculating the Gibbs' free energy of the tubulin heterodimer and gave the command: gmx grompp -f /Applications/md/tutorial/gibbs/MDP/EM/em_steep_0.mdp -c /Applications/md/tutorial/gibbs/1TUB_solv.gro -p /Applications/md/tutorial/gibbs/topol.top -o min0.tpr I got this error: WARNING 1

[gmx-users] 500ns simulation

Hi! What changes do I make to the mdp files provided by you in the lysozyme tutorial, to make it a 500ns simulation? Thanks in advance! Regards, Raag -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

[gmx-users] MPI

Hi! Do you have any tutorials for MPI, please? Regards, Raag -- 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 vi

[gmx-users] topol file inaccessible

Hi! I'm simulating a heterodimer. The simulation goes really smoothly till the MD production step where I get an error saying the topol file is inaccessible. Can you please help? Thank you in advance and regards, Raag -- Gromacs Users mailing list * Please search the archive at http://www.groma

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 171, Issue 84

istinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! >

[gmx-users] topol inaccessible in the production md step

Hi! I'm simulating a heterodimer, with the help of your lysoyme tutorial. The simulation runs smoothly till the production MD step. I gave these commands: gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr time -p mpirun gmx_mpi mdrun -v -deffnm md I kept md.mdp identica

[gmx-users] gmx_dipoles Mtot and aver difference

Hi! I was comparing the dipole moments of a few proteins. The results of the Mtot and the aver files are diametrically opposite to each other. The proteins with the max dipole moments according to the Mtot files, are the ones with the least dipole moments according to the aver files. What is the d

Re: [gmx-users] gmx_dipoles Mtot and aver difference

Hi! I had written earlier that I wanted to compare the dipole moments of a few proteins and that the Mtot and Aver files were giving me diametrically opposite results. The proteins with the highest dipole moments according to Mtot were the ones with the lowest dipole moments according to aver and

Re: [gmx-users] gmx_dipoles Mtot and aver difference

I gave the following commands: gmx_mpi trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center (I first selected 0 and then 1, like in the lysoyme tutorial). gmx_mpi dipoles -f md_noPBC.xtc -s md.tpr Despite that, I am getting opposite values in Mtot and aver. By re-center do you mean som

[gmx-users] Place a gap in y-axis

Hi! This is not really a gromacs question, but I was wondering if you could help, please! I have a multiple line plot with a major difference between one of the plots and the rest. Hence, I need to insert a gap in the y axis. I usually use grace to plot the graphs generated by gromacs, but I’m una

[gmx-users] Selection of residues in one of the chains of heterodimer

Hi! I simulated a heterodimer and converted the md.gro file into a pdb file. This pdb file I visualised in vmd. I wish to select residues (first 50, then next 50 and so on), so that I can correlate the structure with the graphs obtained by structure analysis. If I give the command resid 1 to 50 an

Re: [gmx-users] Selection of residues in one of the chains of heterodimer

Hi! The gro file lost the data about the chains and treated the entire heterodimer as one chain. Anyway, problem solved! I checked the atom numbers from the gro file and selected those in VMD. A bit tedious, but worked! Thank you and regards, Raag -- Gromacs Users mailing list * Please search t

[gmx-users] standard error

Hi! What percent error is calculated as standard error by gmx analyze? 5%? Thank you in advance and regards, Raag -- 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/

[gmx-users] addition of an isopeptide bond and its simulation

Hi! I need to study the effect of post-translational modifications on the biophysical properties of my protein. This involves the addition of an isopeptide bond to the primary chain of the C-terminal tail. How may I add this isopeptide bond? And then which force field can I use to simulate it?

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 156, Issue 112

? ?) >4. Hbond residence time (Marcelo Dep?lo) >5. addition of an isopeptide bond and its simulation (Raag Saluja) >6. CG Graphene - dihedral problem/parameter (Sajjad Kavyani) >7. Re: User Defined Potentials (Vytautas Rakeviius) > > > ---

[gmx-users] force field for acetylated protein pdb file

Hi! I acetylated K40 my heterodimer's PDB file using PyTMs in PyMOL. Now I need to simulate it using GROMACS. Which force field would be the best for this purpose? Thank you in advance! Regards, Raag -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/M