[gmx-users] angle

Dear gmxusers I want to calculate the angle between 2 alpha helix. One of the possibility to do, is g_bundle command. If I want to use g_bundle I have a problem to define the groups in the index file. On a basis of which criteria could I choose the 3 group in index file as input for g_bundle??? B

[gmx-users] angle

Dear gmxusers I want to calculate the angle between 2 alpha helix. One of the possibility to do, is g_bundle command. If I want to use g_bundle I have a problem to define the groups in the index file. On a basis of which criteria could I choose the 3 group in index file as input for g_bundle??? B

[gmx-users] DNA SIMULATION

Dear gmxuser Does somebody knows how to simulate the DNA in gromacs?? I know it is so general question but I need some hint. Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search t

[gmx-users] POSITION-RESTRAIN

Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file "posre_entirelipid1.itp", line 56 ]:

[gmx-users] Position-restraint

Dear gmx-users, I am trying to create a tpr file using grompp. My system has a protein with four identical chains, 288 POPC molecules, SOL, and ions. I am trying to restrain the lipid molecules. When running grompp, I get the following message: Program grompp, VERSION 3.3 Source code file: top

[gmx-users] minimization

Dear users I want to minimized a dimer protein but at the first step it start to explosion. I tried to decrease the dt but it is not working. the protein is in the high energy level. Is there any suggestion how to minimized such a high energy level protein?? thanks __

[gmx-users] minimization

Dear users I have a dimer protein which I want to minimized it..unfortunately the protein is in high energy level and before starting to minimize it explode. I already went through users email and also wiki gromacs and also I tried all the way like changing time step, change coulomb type ,... but

[gmx-users] minimization

Dear users I have a dimer protein which I want to minimized it..unfortunately the protein is in high energy level and before starting to minimize it explode. I already went through users email and also wiki gromacs and also I tried all the way like changing time step, change coulomb type ,... but

[gmx-users] minimization

Dear users I have a dimer protein which I want to minimized it..unfortunately the protein is in high energy level and before starting to minimize it explode. I already went through users email and also wiki gromacs and also I tried all the way like changing time step, change coulomb type ,... but

[gmx-users] minimization

Dear Tsjerk Thanks for your suggestion...actually It is a crystal structure...the problem happen when I want to minimize the structure in vacuumthe box size is enough...but the problem is that the minimization is fine with gromacs forcefield but it is not ok with OPLSAA forcefiledI tried t

[gmx-users] minimization

ect or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..."

[gmx-users] minimization

Dear MARK and Tsjerk I found somethingafter making topology file by pdb2gmx ... I made tpr file by grompp ... then I give the original pdb file and tpr file to ngmx to see the system before running minimization...the interesting thing was that the bonds between atoms are stretched.. I comp

[gmx-users] -symm option

Dear all does somebody knows how -symm option from g_density command do the calculations? Or in other word what is the basic of -symm option? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.

[gmx-users] covariance

Dear gmxuser I want to compare a dimer covariance which was already run in 2 different situation. The problem is that the scale of produced covariance (which produced by -xpma) in 2 case is different e.g the scale for one of them start from -0.18 to 0.05 and other -0.15 to 0.052. Is there any poss

[gmx-users] covariance

Dear Tsjerk Thanks for your help and reply. I thing my question was not clear. I want to compare 2 covariance map. but in one map the red colour shows e.g 1 nm^2 fluctuation and in other map the red colour shows e.g 0.5 nm^2 fluctuation. I wanted that both map be in the same scale of colour inten

[gmx-users] surface amino acids

Dear gmxusers I would like to find the amino acids which are on the surface of protein. Is somebody knows any script or software to do that? thanks in advance M -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] see some line in vmd

Dear gmx user I have a box which contain protein and solution. Before running I minimized it very well and also system is running. After 2 ns when I saw the trajectory in vmd I saw that ther is some lines like bondes in the system. eg, between oxygen group of one water molecule in one part of box

[gmx-users] X2top

Dear gmxusers I want to make a itp file by x2top command. but unfortunately It does not work. I receive the following error: Fatal error: Library file ffoplsaa.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) I check t

[gmx-users] x2top

Dear Dr,van der Spoel I am using the 3.3.2 version. It is totally installed. I used echo $GMXDATA but it did not show anything. Thanks for your help Morteza ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

[gmx-users] how long it take to run do_dssp

Dear gmxuser I want to analyze the secondary structure of a protein after a 10ns simulation run but I do not know how long it will take because I run it for more than 2 hours but it is still running.I don't know whether I am encountering any problem , in the manual it is mentioned that the progra

[gmx-users] do_dssp

Dear gmx users, I run the program do_dssp for my system which is too small. Unfortunately, I run it for a long time but I am in a doubt that it is working correctly or not because it is run for one day and i don't have any idea when it will be finished and also after running I have a message which

[gmx-users] do_dssp

Dear florian thanks for your help. I installed the DSSP in the root. It is working well when I run ./dssp in DSSP directory. It seems that the program don't have any problem. As you said I already set an environment also but any of them did not working. It made me crazy that everything is ok, Insta

[gmx-users] do_dssp

Dear gmxuser, I ried the do_dssp command to analyses my protein structure. It produce scount.xvg ans ss.xpm file. I could see xvg file by xmgrace and ss,xpm by GIMP software. Till now everything is ok. But when I want a make post script file by xpm2ps for producing plot.eps file I get the followin

[gmx-users] FATAL ERROR: x2top

Dear gmxuser I wan to make itp file to use opls forcefield. When I use x2top, I took the following error: Fatal error: No forcefield type for atom CAA (1) with 4 bonds what should be the problem? thanks ___ gmx-users mailing listgmx-users@gromacs.

[gmx-users] NO such a molecule type

Dear gmx users I want to run the system by OPLS forcefield. My system has protein, water and 1 ligand (Boromohexane) and NA. At the first I put the protein in the water and minimized it then add the ligand to system. I already made a itp file for the ligand. I add the ligand itp file to the topol

[gmx-users] NO such a molecule type

Dear Mark, Thanks for your help. As you said I define cpp path for my system. Now I get 1 warning and the following error. To be mor clear, I also paste my mdp file. checking input for internal consistency... WARNING 1 [file md_bfgs.mdp, line unknown]: Removing the rotation around the center of

[gmx-users] No such a molecule

Dear mark you were right. I checked my itp file and i see that I defined force field in the itp file also. By ignoring the forcefield in itp file I get proper respond. thank you very much for your help ___ gmx-users mailing listgmx-users@gromacs.

[gmx-users] (no subject)

Dear gmx user, I want to simulate one cytochrome protein inside the water box. Unfortunately in the stage of pdb2gmx I faced with the following error: Residue 'HEME' not found in residue topology database How could I involve heme group? Before thanks ___

[gmx-users] freez group

Dear Users, I have a ligand inside one protein which I should freeze them to equilibrate the solution around the protein. Unfortunately after some ps the structure of protein and the environmental solution start to crash to each other. Before I start mdrun, after grompp I get the following error:

[gmx-users] freez group

Dear Mark, thanks for your suggestion...the position restrain is very good idea which I did it before..but I just restrain protein and after some time ligand start to come out..I think my problem is that I don't know how to restrain ligand? It will be nice of you if tell me how to restrain ligand?

[gmx-users] density around protein

Dear gmxusers I want to calculate the density of solvent around protein. I already tried the commands g_density and g_densmap but the results are not the the things that I want. The g_density Compute partial densities across the box and g_densmap just give me one black and white photo which don't

[gmx-users] solvent density around protein

First thanks Matt to reply me for my problem. As I say I want to calculate the density of solvent around protein. I already tried the commands g_density and g_densmap The g_density Compute partial densities across the box and g_densmap just give me one black and white photo which don't have sense.

[gmx-users] g_sdf

Dear gmax user I want to use G_SDF command. But the description of this comand is alittle bit complicate for me. I want to compute the density of water around protein and I dont know could I do it or not. I will be thankful if somebody suggest me by this command. Thanks _

[gmx-users] g_sdf

Dear Dr.Warren Thanks for your help about g_sdf. Actually I am confused about determine of the atoms (three reference atoms for the molecule) in index. I don't know on a basis of which criteria should I choose this three atoms inside the protein? Before thanks ___

[gmx-users] Disappear my solution

Dear I have a box with 2 different kind of solution and one protein. Actually, I minized my box in each step which i add matter to box. After minimization of my system I run it for 10 ns. unfortunately after 1.3 ns one of my solution dissapear. eg, I have hexan organic solvent, water and protein,

[gmx-users] Disappear my solution

Dear Thanks for your prompt reply. In gro file everything is ok. during the run I just load my XTC file by vmd visual software and i saw that after 1.3 ns suddenly hexan disappear and my system just have protein and water. the most strange things is that the place of hexan is empty and is not full

[gmx-users] Disappear my solution

Dear Justin Thanks for your helps. --Did you restart your run after that short time? Did you change the xtc-grps option in your .mdp file? no. I did not change any option and also not restart my run. --That would be pretty strange. If they were there, then disappeared, maybe they were not

[gmx-users] Disappear my solution

Dear Justin Thanks for your prompt reply and guide. As you said I checked my files with gmxcheck. My tpr file is ok. It includes water, hexan and protein. but my edr, xtc and trr files have problem. Their faults are as follow: 1- for xtc: Reading frame 110 time 550.000 Fatal error: Magic

[gmx-users] How generate top file with all hydrogen atomes

Dear I have been trying to use the PRODRG server to generate GROMACS topology files for some organic molecules.But unfortunately the PRODRG server automatically deletes all hydrogens and only (re)creates "polar" hydrogens. However, I also want to "keep" the H atoms conected to the aromatic carbons

[gmx-users] OPLS force field does not recognize Atom type

Dear I want to make the solution which is not working with unified atom force fields. Then I decided to make the itp file by my own. I made the all atom type itp file for opls AA. I found all of the opls feature in gromacs top directory and according to the top directory files I made the new it

[gmx-users] OPLS force field does not recognize Atom type

Dear As you said I change the name of the itp file to opls_xxx. It works. thank you very much. But now i faced with new problem. I got new error: Fatal error: Incorrect number of parameters - found 4, expected 6 or 12. what does it mean? Thank you in advance Morteza __

[gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.

Dear justin, I have made the itp file on a basis of chapter 5 of gromacs. Every things seems fine. my itp file for opls is as follow: ; [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_185 1 DRG HAD 10.02

[gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.

Dear Justin, thanks for your help. The last lines of my grompp are: checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 pa

[gmx-users] system couldn't be run

Dear I make the solution box of organic solvent. It is homeogen and mixed properly. It also has a minimum energy. I put one protein in this solution. Before put the protein in the solution I minimimized it also. Now I mixed 2 system which each of them are minimized. After put the protein in the so

[gmx-users] pdb_to_xvzr not working

Dear I want make hole in my system. Because of this I oblige to use MSMS programm to calculate the surface of my protein. Before using MSMS we should change pdb file format to xyzr file format. I should use pdb_to_xvzr to produce xvzr file. Unfortunately I couldn't run pdb_to_xvzr. After running

[gmx-users] system exploid during running

Dear gmxuser Thanks for your advices. Because of your help I could run my solution and protein together. but during the run I faced with this warning which cause the run again be crashed, The message is: relative constraint deviation after LINCS: max 0.000615 (between atoms 1731 and 1732) rms 0.0

[gmx-users] still system exploid

Dear gmx user I tried everything that you offer me to run my solution. I tried to assess my system by ngmx before running. I realized that my system is exploided befor starting EM. I tried the followinf mdp files: 1-;Enegry minimization cpp = cpp define = -DPSRES integrator =

[gmx-users] still system exploid

Dear gmxuser, Thanks for your all helps. But still I have problem. As you friend said I increase the vdw and box size and also i decrease the time step till 0.0001 but unfortunately system crash befor EM running. I do check with ngmx. To reply the question that said what is your system? My system

[gmx-users] PBC

Dear users I have a dimer protein in the water box. It was run for 30ns. during the simulation dimer split to two monomer. This things happen bc of PBC. ( I checked it by vmd pbc option ) to have a two monomer together during trajectories (for visualization) I have used the following command: trj