[gmx-users] (no subject)

-- 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 requests to the list. Use the www interface or send it to g

[gmx-users] pulling along hexane-water interface

yed a bit with the pull rate and pull constant, but same thing happens. Are we doing something wrong? Can you please help? -- Prithvi Raj Pandey National Chemical Laboratory, Pune 411008. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Ple

[gmx-users] (no subject)

ame thing happens. Are we doing something wrong? Can you please help? -- Prithvi Raj Pandey National Chemical Laboratory, Pune 411008. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.

[gmx-users] water mediated hydrogen bond

Hi all, I would like to measure the water mediated hydrogen bond between the ligand and the protein. When I searched the forum I could able to get the link (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt) for the script with which we can get the above mentioned obje

[gmx-users] Re: hydrophobic contacts

Hi all thanks for your valuable suggestions. But still i'm not clear. I have tried using the .tpr file with make_ndx but the index group is displayed is similar to that of the one with .gro file. I have manually identified the residues and when i ran the g_mindist with the ligand 0f 18 atoms again

[gmx-users] Re: hydrophobic contacts

Hi all, can some one tel me how can i prepare a index file specifying the hydrophobic atoms along for measuring the hydrophobic contacts in the systems alone. -- View this message in context: http://gromacs.5086.n6.nabble.com/hydrophobic-contacts-tp4998153p5002931.html Sent from the GROMACS Us

[gmx-users] Re: g_mindist - reg

Hi, can you suggest me how can i identify or specify the hydrophobic atoms to the index files. -- View this message in context: http://gromacs.5086.n6.nabble.com/g-mindist-reg-tp5000756p5002819.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing lis

[gmx-users] Re: g_mindist - reg

thank you justin ... I have given the entire protein as one group.. now will it be ok or i need to give only hydrophobic resides alone as a index group. Thank you once again for yor response -- View this message in context: http://gromacs.5086.n6.nabble.com/g-mindist-reg-tp5000756p5000771.htm

[gmx-users] g_mindist - reg

hi all, I would like to measure the hydrophobic interaction of the ligand against the protein during the simulation . From the forum I learnt g_mindist will be the better tool. But when i used the command g_mindist -f traj.xtc -s topol.tpr -n index.ndx -on numcont.xvg -group and selected protein

[gmx-users] write velocity and coordinates with template.c

in; charset=ISO-8859-1; format=flowed > > On 26/07/2012 8:22 PM, prithvi raj pandey wrote: >> Dear gmx users, >> >> I am using template.c of gromacs 4.0.7 for writing my own analysis >> tool. When I am using the fr.x[i][XX], it writes the coordinates of >> th

[gmx-users] Writing velocity of particles using template.c

Dear gmx users, I am using template.c of gromacs 4.0.7 for writing my own analysis tool. When I am using the fr.x[i][XX], it writes the coordinates of the particles (i crosschecked it with the coordinates written by the trjconv command). But the problem arises when I use fr.v[i][XX] for writing th

[gmx-users] position restraints in SMD

Hi all, It may be naive but I would like to get some clear explanation in SMD ( COM pulling) reg. The question is, Before performing the COM-pulling (incase of protein ligand complex) do we need to position restrain the ligand using genrestr and then add the topology to the topol.top file. If not

[gmx-users] water bridge

Hi all, I have an protein and drg complex. I've done the MD in SPC water environment. Now I would like to check number of hydrogen bond formed between the drug and protein, water as well. What will the right command for me to analyse. Thanks in advance -- View this message in context: http://gro

[gmx-users] Re: specifying the direction of Pull in US

Thanks for ur suggestion Justin, I'm facing trouble in setting that vector, actually I cant figure out how can i set up a vector. Is there any easier way with which i can set up a vector. Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/specifying-the-direction-of-Pull-i

[gmx-users] Re: specifying the direction of Pull in US

hi , When i applied distance I cant have control over the direction of the pull. The ligand is not exactly pulled along the direction i meant to pull -- View this message in context: http://gromacs.5086.n6.nabble.com/specifying-the-direction-of-Pull-in-US-tp4999140p4999155.html Sent from the GRO

[gmx-users] specifying the direction of Pull in US

Hi all, I am working on steered molecular dynamics and In that I would like to pull the ligand ( already in complex with protein) away from the reference amino acid ( which I've selected so that I can direct the ligand to get closure to my desired amino acid residue). Now the thing is when I used

[gmx-users] Re: chi1/chi2

Dear Mark, Thanks for your reply.. can you suggest me how i can take the plot with 0 to 360 angle. I've tried periodic of g_chi with -all option to generate the chi1/chi2 plot for the each and every amino acid residue but i couldnt do it properly can you suggest on this. Thanks in advance -- View

[gmx-users] Re: COM Pulling

Dear Justin, I've tried what you have suggested. I have used the pull code and gave 4 amino acid residues as a reference group. The location of the groups are one below the ligand (in the protein core) and 3 were on the above ( towards the active site gorge). When i used the code pull

[gmx-users] Re: COM Pulling

Thanks for your reply Justin. >From your umbrella tutorial I thought the reference group should be the protein. Now from your reply i think I can specify any amino acid residue in the protein and I can drive the ligand towards the residue. where I need to specify the group If i'm using the pull c

[gmx-users] COM Pulling

HI , I have been performing SMD after reading bevan lab tutorial. The tutorial was very informative in basic aspects. Now I have my ligand inside the protein and I wan to pull it out in a specific direction. I applied force separately along the X, Y and Z axis . In which none of the pull seems to b

[gmx-users] chi1/chi2

during the simulation. I tried g_chi to obtain chi1 and chi2 values at the end I'm getting the plot withe values ranges from -180 to 180 . But in papers people have reported in 360 degree how can i get the data. Please give me suggestions -- View this message in context: http://gromacs.5086.n6

[gmx-users] Error in atom type

Dear users, Force field: 53a6 water model: spcTermini : NH3+ and COO- After the command:pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top -ter -merge -ignh I have the following error: Fatal error: Fatal error: Atom LPG1 in residue CYS 143 was not found in rtp entry CYSH with 8 atoms while sorti

[gmx-users] atomic concentration in x and y axis

hether the elimination of translational and rotational motions is enough to calculate this property, should I have to align the structure in the z axis using the PCA analysis? Regards, Raj. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

[gmx-users] concentration distribution

Hello, I would like to calculate the concentration distribution of atoms along the x and y axis from the trajectory. Can anybody suggest me a tool to calculate this? regards, Raj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] solvation box type for nanotubes

Hello, Can we use rhombic dodecahedron solvation box for the PMF calculation on the small molecule diffusion into carbon nanotube. so that we can reduce 29% calculation time. If so then what could be the box size? Thank you. Regards, raj -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Intermolecular RDF in DPPC

file /export/softexport/gromacs/share/gromacs/top/spc.itp Excluding 49 bonded neighbours molecule type 'DPPC' and does not proceed further. What is wrong? Can anyone please help? -- Prithvi Raj Pandey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

[gmx-users] Problem with g_density

were done using the folloing tool g_density -f-o -n -s -d Z Can anyone help? -- Prithvi Raj Pandey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting