[gmx-users] Trying to obtain dcd files

Hello, I am a new user to vmd and I wanted to know how to generate dcd files. Reading from posts that already exist here about dcd file generation, I found out that we can use wordom to do this generation which when I tried to configure in linux, didn't work. I got some help thinking this was my

[gmx-users] Trying to get dcd files

Hello, I am a new user to vmd and I wanted to know how to generate dcd files. Reading from posts that already exist here about dcd file generation, I found out that we can use wordom to do this generation which when I tried to configure in linux, didn't work. I got some help thinking this was my

[gmx-users] transfering files from host computer to lyceum

Hi, I am a new user to linux, lyceum and gromacs. I was just wondering if anyone knew what exactly to do to transfer files from the host computer to lyceum? I really need help. Thanks in advance, Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/transfering-files-from

[gmx-users] topology and coordinate file not matching after grompp

Hello, I have a problem and although I've read almost everything the internet could offer on how differently people have approached this problem, mine hasn't been solved yet. Basically, I am trying to mix 2 different proteins in one box and after doing my grompp to neutralise the system, I get th

[gmx-users] Re: topology and coordinate file not matching after grompp

Thanks Justin. So, I've understood how to calculate the number of coordinates. That in the topology file matches the amount I calculated (as per how you just taught me). I want to put 2 proteins in the same box. I did this by changing the topology files of the respective proteins to itp. Then a ne

[gmx-users] Re: topology and coordinate file not matching after grompp

Hi Justin, Oh, I see. I am going to paste my commands here. pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0 editconf -f 2CDS_conf.gro -o conf1.gro -center 7.5 0 0 cat conf1.gro conf2.gro

[gmx-users] Re: topology and coordinate file not matching after grompp

renumber.gro topol_1AKI.itp topol_2CDS.itp I get the feeling you're not going to be able to see the

[gmx-users] Re: topology and coordinate file not matching after grompp

Thank you very much Justin. It's working fine now :) Really appreciate it. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010255.html Sent from the GROMACS Users Forum mailing list archive at Nabble.c

[gmx-users] Re: topology and coordinate file not matching after grompp

I actually have another problem. When doing my grompp for nvt equilibration, I egt the error, Topology include file "posre.itp" not found. In my topology file I wrote this: ;Include the force field #include "oplsaa.ff/forcefield.itp" ; Include chain topologies #include "topol_1AKI.itp" #include

[gmx-users] Re: topology and coordinate file not matching after grompp

Right, I've understood that now. I've altered all of that. But somehow, the same error message still appears.. -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010259.html Sent from the GROMACS Users Forum ma

[gmx-users] Re: topology and coordinate file not matching after grompp

oh, sorry. So the error is: Fatal error: Topology include file "posre.itp" not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The command I typed: grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr My topo

[gmx-users] Re: topology and coordinate file not matching after grompp

Hi Justin, Yes that was a problem. So after modifying my #include statement in the itp file (initially top. file), it became: ; Include Position restraint file #ifdef POSRES #include "posre_2CDS.itp" #endif thank you Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/

[gmx-users] Re: topology and coordinate file not matching after grompp

Hi Justin, The simulation is running fine for this task. There's something additional I want to do and I'd like to know how you'd approach it. I want to add charges to each of the protein so that I can observe how the respective protein interacts with their respective charge cloud. The proteins im

[gmx-users] Re: topology and coordinate file not matching after grompp

Hi Justin, The simulation is running fine for this task. Thank you for helping me There's something additional I want to do and I'd like to know how you'd approach it. I want to add charges to each of the protein so that I can observe how the respective protein interacts with their respective char

[gmx-users] Adding charges to a protein to observe interaction

Hi, I have a box with 2 proteins in them. I want to add charges to each of the protein so that I can observe how the respective protein interacts with their respective charge cloud. The proteins I'm using are 2CDS.pdb and 1AKI.pdb from the RCSB bank. > >From what I figured, I tried using genion u

[gmx-users] Lennard jones energy

Hi all, Can someone please guide me on how I can use g_energy to print Lennard Jones energy? Thank you so much in advance. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/Lennard-jones-energy-tp5010564.html Sent from the GROMACS Users Forum mailing list archive at N

[gmx-users] error with g_dist

Hello all, I am trying to find the distance between 2 centres of mass using g_dist. I use the command: g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx but i get the error: Fatal error: Molecule in topology has atom numbers below and above natoms (1707). You are probably trying to use

[gmx-users] Re: error with g_dist

I'm basically trying to see how the distance between the ligand and protein changes with time using their centres of mass and the only way I've come across is by using g_dist. I'm pasting the contents from the terminal after the doing a gmxcheck on the md_0_1.xtc file which is my .xtc file from th

[gmx-users] Re: error with g_dist

Oh, sorry sorry. I see what your asking. I asked for 2 groups. One being the protein and one being the ligand (JZ4) screenshot.png sorry, you may have to zoom in. I'm not sure how to snip on linux still. Chinnu -- View this me

[gmx-users] Re: error with g_dist

1 and 13 Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010742.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] Re: error with g_dist

No, I chose 1 and 13. I just tried again, but the error is still the same.. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010744.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx

[gmx-users] Re: error with g_dist

I've copy, pasted the text after selection: eading file md_0_1.tpr, VERSION 4.5.5 (single precision) Group 0 ( System) has 33037 elements Group 1 (Protein) has 1693 elements Group 2 ( Protein-H) has 1301 elements Group 3 (C-alpha) has 163 elements G

[gmx-users] Re: error with g_dist

md_0_1.tpr - production simulation .tpr file 3HTB_clean.pdb - .pdb file after removing hz4 coordinates JZ4.pdb

[gmx-users] Re: error with g_dist

Mine still gives me the same error. I don't quite understand why since it's giving u the right output. Im using the same version as you too. If you do not mind, could you give me the .xvg file? So that I can use it as a result. Simultaneously, I'll see what I can do to solve the problem with your

[gmx-users] Re: error with g_dist

ok that's ok then. this was the school system. so I can't really reinstall it. I'll try and use a cluster. Hopefully, it works. thanks a lot Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010751.html Sent from the GROMACS Users Forum mai

[gmx-users] Re: error with g_dist

I won't be submitting these though. just letting you know. I just need to explain how all of these can be achieved. Just clarifying. But thank you for all the help you've provided. It's been very valuable help. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/error-wi