[gmx-users] try2

try2 -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un

[gmx-users] the effect of ligand on protein

eigenvectors Are these analyzes adequate? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

[gmx-users] Re: the effect of ligand on protein

Dear users, any suggestion? Thanks in advance 2012/7/2 ahmet yıldırım ahmedo...@gmail.com Dear users, Which analysis do you suggest to examine the effect of ligand on protein? 1.)For quality assurance: RMSD,RMSF and Radius of gyration for free and complex form 2.)For structural

[gmx-users] content of secondary structure output file

84139 165 0 6 1 ... -- Ahmet Yıldırım -- 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

Re: [gmx-users] Regarding RMSD analysis result

/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Regarding RMSD analysis result

/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] tpr file

? Thanks in advance -- Ahmet Yıldırım -- 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

[gmx-users] regarding converge of system

as an indicator of convergence of the structure. are there other indicators of convergence of the structure? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

Re: [gmx-users] regarding converge of system

indicators of convergence of the structure? Thanks in advance -- Ahmet Yıldırım -- 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

[gmx-users] cosine content and nonconverged trajectory

Groot). What is a high cosine content? 0.2, 0.5 or 0.7 What is the value? Thanks in advance -- Ahmet Yıldırım -- 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

[gmx-users] increase of temperature or pressure

in temperature or pressure? What are your suggestions for the solution? Thanks in advance -- Ahmet Yıldırım -- 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

[gmx-users] coordinates obtained from the Automated Topology Builder

interactions, which coordinates I use? Optimised coordinates obtained from the Automated Topology Builder or original coordinates in .pdb? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

[gmx-users] activation energy

Dear users, Is it possible to calculate the activation energy of a structure using Gromacs? if OK, how? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

Re: [gmx-users] activation energy

energy. What definition do you use? On 01/14/2013 01:15 PM, Ahmet yıldırım wrote: Dear users, Is it possible to calculate the activation energy of a structure using Gromacs? if OK, how? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman

[gmx-users] suffice of position restraints

Dear users, I usually apply the positions restraint of 100 ps on system. Does it produce a problem to apply the positions restraint for long time (100 or 200 ps)? cant it cause strain on structure? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Re: Reference structure for PCA.

requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

Re: [gmx-users] compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition

! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] diffusion constant level off

of D and c? 4.) What should be Time between restarting points in trajectory? Thanks in advance -- Ahmet Yıldırım -- 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

[gmx-users] Re: diffusion constant level off

Ahmet yıldırım ahmedo...@gmail.com Dear users, I used the following commands to get diffusion constants (every 10 ns) of a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory every 20 ps). I looked at RMSD vs average structure, RMSD vs starting structure, Radius

Re: [gmx-users] Re: diffusion constant level off

, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s

Re: [gmx-users] Re: diffusion constant level off

as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel sp...@xray.bmc.uu.se On 2013-03-28 10:40, Ahmet yıldırım wrote

Re: [gmx-users] Re: diffusion constant level off

Please see plot: http://imageshack.us/photo/my-images/35/diffusion.png/ 2013/3/28 Justin Lemkul jalem...@vt.edu On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering

Re: [gmx-users] RE: diffusion constant level off

/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- 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

[gmx-users] water models tip3p.gro and spce.gro

Dear users, I will run MD simulations of all water models in Gromacs. I need spce.gro and tip3p.gro files. How can I find them? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

[gmx-users] tip5p water model:Atomtype LP1 not found

1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

[gmx-users] thermal conductivity,specific heat,enthalpy

35 #Surf*SurfTen 36 Mu-X 37 Mu-Y38 Mu-Z39 T-System40 Lamb-System Firstly I calculated Entalphy (16) Afterward I calculated both Etot (7) and pV (15) Enthalpy=Etot+pV Unfortunately, I get Enthalpy isnt equals to Etot+pV. Why? -- Ahmet Yıldırım -- gmx-users

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7. are they wrong? 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear Justin, I copied to gmx.ff it. You know the tip5p shows

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt find them 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

minim.mdp -c protein-water.gro -p protein.top -o protein-water.tpr Fatal error: number of coordinates in coordinate file (protein-water.gro, 37090) does not match topology (protein.top, 34530) 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 7:28 AM, Ahmet yıldırım

[gmx-users] Re: thermal conductivity,specific heat,enthalpy

could anybody help me please? 2013/4/11 Ahmet yıldırım ahmedo...@gmail.com Dear users, I calculated diffusion constant of a substance using g_msd tool. I also want to calculate thermal conductivity its. By the way,I did npt simulation. Diffusion constant=alpha Thermal conductivity=k

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

There isnt the number of water molecules in topol.top after genbox command. I dont understand why they have been deleted. 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I got tip5p.gro from

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? 2013/4/15 Justin Lemkul jalem...@vt.edu On 4/15/13 6:58 AM, Ahmet yıldırım wrote: I have the following files in directory 1.tip5p.gro 2.topol.top 3.em.mdp topol.top: #include oplsaa.ff/forcefield.itp

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

+01 2013/4/15 Justin Lemkul jalem...@vt.edu On 4/15/13 7:22 AM, Ahmet yıldırım wrote: I did as you said. I corrected number of water molecules in the topology by hand. grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Steepest Descents converged to Fmax

Re: [gmx-users] Re: thermal conductivity,specific heat,enthalpy

/msg37580.html; cP = (H^2 - H^2)/kB T^2 (NPT sim) This formula doesn't equal to equation 13. There isnt H^2 term in equation 13. Why? Thanks in advance 2013/4/12 David van der Spoel sp...@xray.bmc.uu.se On 2013-04-11 22:20, Ahmet yıldırım wrote: could anybody help me please? Check http

[gmx-users] g_analyze error bar

Dear users, g_analyze -f rmsd.xvg -av average.xvg -errbar stddev Unfortunately, this command didn't produce the error bar How can I obtain error bar for plotting? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] g_analyze error bar

First column is time, second is rmsd value and third column is 0. average.xvg 10 0.3123 0 20 0.3256 0 30 0.3981 0 40 0.3512 0 50 0.3754 0 ... 2013/4/16 Justin Lemkul jalem...@vt.edu On 4/16/13 4:26 PM, Ahmet yıldırım wrote: Dear users, g_analyze -f rmsd.xvg -av average.xvg -errbar stddev

[gmx-users] rotation of a ligand

Dear users, I have a ligand bound to protein. How can I calculate how much this ligand is rotated during the simulation time? Which tool should I use? g_order, g_chi, g_dih? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Re: rotation of a ligand

topol.tpr -n order.ndx -order.xvg Fatal error: grp 1 does not have same number of elements as grp 1 What should I do? 2013/5/3 Ahmet yıldırım ahmedo...@gmail.com Dear users, I have a ligand bound to protein. How can I calculate how much this ligand is rotated during the simulation time? Which

[gmx-users] multi file input for index files

. Gromacs tools do not support multi file input for index files from http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html. Is this correct? If no, what should I do? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] multi file input for index files

Hi, But I want to calculate the hydrogen bonds between A and B groups. If I do as you said, I will have calculated intra hydrogen bonds of a group AB (merged A and B). 2012/1/10 Mark Abraham mark.abra...@anu.edu.au On 10/01/2012 7:13 PM, ahmet yıldırım wrote: Dear users, I created two

Re: [gmx-users] multi file input for index files

-- *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [ahmedo...@gmail.com] *Sent:* Tuesday, January 10, 2012 8:13 AM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] multi file input for index files Dear users, I created two

Re: [gmx-users] Error in installation

(un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] overheating problem

Dear Mark, Believe me, I tried all methods that you said but unfortunately the result doesnt change :( 2012/2/4 Mark Abraham mark.abra...@anu.edu.au On 4/02/2012 8:24 AM, ahmet yıldırım wrote: Dear users, I am using ubuntu 11.1 (64 bit). The Ubuntu normally runs when I dont run

Re: [gmx-users] overheating problem

Hi, The problem might caused by X58 chipset. Now I am using ubuntu. Which operating system do you recommend? 2012/2/4 David van der Spoel sp...@xray.bmc.uu.se On 2012-02-03 23:49, ahmet yıldırım wrote: Dear Mark, Believe me, I tried all methods that you said but unfortunately the result

Re: [gmx-users] overheating problem

Hi, I put a new cooler (Thermaltake Friock) on the CPU. The problem is solved. 2012/2/4 Mark Abraham mark.abra...@anu.edu.au On 4/02/2012 11:15 PM, ahmet yıldırım wrote: Hi, The problem might caused by X58 chipset. Now I am using ubuntu. Which operating system do you recommend? I doubt

[gmx-users] rerun problem

appended to new files (traj.xtc, ener.edr, md.log). What should I do? Cheers, -- Ahmet Yıldırım -- 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

[gmx-users] one ligand in ATB

coordinates when it obtains .gro and .itp files. can I use these files obtained from ATB? If ok, doesn't the location/position of the ligand change in the enzyme? Greetings -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] pme note

Dear users, I get the following note: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing What should I do? Thanks in advance -- Ahmet Yıldırım

[gmx-users] Neigborsearching, Electrostatics and vdw options

FOR ELECTROSTATICS AND VDW coulombtype = PME pme_order = 4 fourierspacing = 0.16 *rcoulomb = 0.9 * vdw-type = Cut-off *rvdw = 1.4* ... Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users

[gmx-users] Re: Neigborsearching, Electrostatics and vdw options

in advance 21 Mart 2012 20:53 tarihinde ahmet yıldırım ahmedo...@gmail.com yazdı: Dear users, I have two configuration as the following related to Neigborsearching, Electrostatics and vdw options. I checked the literature: Generally the rlist, rcoulomb and rvdw have used as the following. rlist=1

Re: [gmx-users] Re: Neigborsearching, Electrostatics and vdw options

(and probably also 4.6.2) in the Gromacs Manual. The Difference between rcoulomb (or rvdw) and rlist is a buffer-zone for the fact that the neighbor-lists are only updated every nstlist steps (often nstlist = 5). Oliver 2012/3/21 ahmet yıldırım ahmedo...@gmail.com: Dear users, Berk Hess says

[gmx-users] parameters of em.mdp

constant of the reaction field ; VdW vdw-type= Cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.4 ; [nm] distance for LJ cut-off ; Bonds constraints = none ; convert all bonds to constraints -- Ahmet

Re: [gmx-users] parameters of em.mdp

= 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 Then, Why did you change some parameters (nstlist,rlist,rcoulomb,rvdw) for energy minimization? Thanks in advance 23 Mart 2012 19:31 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear users, I am using the Reaction-Field

[gmx-users] renumber charge group

H1TRIS H40.463 1.0080 ; 1.000 ; total charge of the molecule: 1.000 -- Ahmet Yıldırım attachment: TRIS.png-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] the RMSD of Bond lengths, Bond angles, Dihedrals and Impropers

to create index files? Cheers -- Ahmet Yıldırım -- 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

Re: [gmx-users] principal moments of ellipsoid

Hi, BioVEC is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to berendered as ellipsoids. http://www.phas.ubc.ca/~steve/BioVEC/BioVECindex.html 2011/5/10 Mark Abraham mark.abra...@anu.edu.au On 10/05/2011 8:23 PM, lammps lammps wrote: Hi, I

[gmx-users] index file

Dear users, I have two ligands. I created a special index group that merges the protein, LiGA and LİGB. I have the pr.mdp file as the following: ... energygrps = ProteinLİGA_LİGB tc-grps = Protein_LİGA_LİGBWater_and_ions ... grompp -f pr.mdp -p topol.top -c em.gro -n

[gmx-users] NPT and NVT ensembles

Dear Justin, In the first tutorial You said After we arrive at the correct temperature (based on kinetic energies), we will apply pressure to the system until it reaches the proper density. That is, you apply each NVT and NPT ensembles when you did the position restraints. Would not it only be

[gmx-users] protein-ligand interaction

Dear users, I want to investigate *Ligand effect *on the protein . To investigation the interaction of protein-ligand: *RMSD calculations:* 1. a) RMSD of Backbone b) RMSD of Backbone+ligand 2. a) RMSD of Protein b) RMSD of Protein+ligand 3. a) RMSD of Protein-H b) RMSD of Protein-H+ligand Which

Re: [gmx-users] protein-ligand interaction

Dear Justin, You said You can get a per-residue RMSD by using g_rmsf -od to see the effect of the ligand on each residue. 1. Can you explain the difference between what goes into the -o file, and what goes into the -od file? 2. How should I create a index file to see the effect of the ligand on

Re: [gmx-users] protein-ligand interaction

Dear Justin, I used -res flag with the following command but I get pairs of values in the output files. is there any mistake related with the command I used? g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res 2011/5/29 jalem...@vt.edu Quoting ahmet y?ld?r?m ahmedo...@gmail.com:

Re: [gmx-users] protein-ligand interaction

230 0.1206 29 Mayıs 2011 19:28 tarihinde ahmet yıldırım ahmedo...@gmail.com yazdı: Dear Justin, I used -res flag with the following command but I get pairs of values in the output files. is there any mistake related with the command I used? g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od

[gmx-users] the effect of the ligand on each residue

Dear users, I want to see the effect of the ligand on each residue using the following command: g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res Select group(s) for root mean square calculation Select a group: ? Which group should I choose? Thanks in advance -- Ahmet YILDIRIM --

Re: [gmx-users] the effect of the ligand on each residue

tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear users, I want to see the effect of the ligand on each residue using the following command: g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res Select group(s) for root mean square calculation Select a group

[gmx-users] g_mindist

Dear Justin, You said before you can obtain some idea by using g_mindist to calculate hydrophobic and hydrophilic contacts between the protein and ligand. That is, I can explore whether there is hydrophobic or hydrophilic feature of ligand using g_mindist tool. is this correct? I did the

Re: [gmx-users] g_mindist

Dear Justin, can you suggest me published paper related to about hydrophobic and hydrophilic contacts? 03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear Justin, You said before you can obtain some idea by using g_mindist to calculate

[gmx-users] g_sas calculation

Dear users, I want to compute SASA between protein and ligand. *1.)* protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein+ligand) select a

Re: [gmx-users] g_sas calculation

)=(protein)+(ligand)-(protein_ligand)* Thanks 2011/7/3 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Dear users, I want to compute SASA between protein and ligand. *1.)* protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx

[gmx-users] residue SASA

Dear users, I want to calculate hydrophilic and hyrophobic SASA value of each residue in protein. I used a command as the following: g_sas -f run.xtc -s run.tpr -or protein_protein.xvg Select a group for calculation of surface and a group for output select a group: 1 (protein) select a group: 2

Re: [gmx-users] residue SASA

There are hydrophilic and hydrophobic SASA values versus simulation time in the output file (area.xvg). I want to hydrophilic and hydrophobic SASA values versus residue. 2011/7/7 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Dear users, I want to calculate hydrophilic

[gmx-users] if PRODRG calculate incorrectly

Dear users, I have a problem related to PRODRG. Chirality:NO Full charges: YES Energy minimization: NO *İnput file name:TRS.pdb* HETATM 1803 C TRS B 232 38.588 -4.733 65.956 1.00 17.99 C ANISOU 1803 C TRS B 232 2126 1948 2760 -378 45-81 C HETATM 1804 C1 TRS B

Re: [gmx-users] if PRODRG calculate incorrectly

Dear Tsjerk and Justin, Thanks for your reply. I will contact the PRODRG developers. can you suggest anyway/anytool for generating ligand coordinates/topologies? Thanks in advance 17 Eylül 2011 15:58 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear users, I

[gmx-users] meaning of minus potential and buried surface area

Dear users, 1.) During the simulation the mean potential energy is minus (-) value. What does this mean? Why minus? 2.) let's say, Interface/Buried Surace Area (ISA) between protein and ligand was calculated and hydrophobic ISA obtained greater than hydrophilic ISA. What does this mean? No one

Re: [gmx-users] what difference between RMSF and RMDEV

3.) This The reference structure used to remove translational and rotational degrees of freedom is RMSD??? 2011/9/21 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Dear users, g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res With the option -od the root mean square

Re: [gmx-users] meaning of minus potential and buried surface area

Dear Justin, If possible, can you some explain net attraction? Best regards 2011/9/22 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Dear users, 1.) During the simulation the mean potential energy is minus (-) value. What does this mean? Why minus? Net attraction. 2

Re: [gmx-users] if PRODRG calculate incorrectly

and .itp files using PRODRG but PRODRG is giving improper results/output. best regards 2011/9/17 Mark Abraham mark.abra...@anu.edu.au On 17/09/2011 11:28 PM, ahmet yıldırım wrote: Dear Tsjerk and Justin, Thanks for your reply. I will contact the PRODRG developers. can you suggest anyway

[gmx-users] RMSD bonds and angles

Dear users, How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] RMSD bonds and angles

I look at chapter 8 but I didnt found that I want. can you give a hint? Thanks 2011/10/3 Mark Abraham mark.abra...@anu.edu.au On 3/10/2011 10:29 PM, ahmet yıldırım wrote: Dear users, How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? Please start your search in chapter 8

[gmx-users] heteroatom not to be a ligand

Dear users, I have a xxx .pdb including enzyme+X. But X is a cryoprotectant, that is heteroatom, it is not a ligand. I think I shouldn't use a way as Justin tutorial 5. Because X is not a ligand. what should I do? Thanks -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] RMSD bonds and angles

any hints? :( 03 Ekim 2011 22:32 tarihinde ahmet yıldırım ahmedo...@gmail.com yazdı: I look at chapter 8 but I didnt found that I want. can you give a hint? Thanks 2011/10/3 Mark Abraham mark.abra...@anu.edu.au On 3/10/2011 10:29 PM, ahmet yıldırım wrote: Dear users, How can I

Re: [gmx-users] RMSD bonds and angles

No, it calculates with respect to the positions atom. but I want to calculate the RMSD bonds (A˚ ) and RMSD angles (o). 2011/10/4 Mark Abraham mark.abra...@anu.edu.au On 4/10/2011 7:05 PM, ahmet yıldırım wrote: any hints? :( You didn't find something useful in the section titled Root mean

[gmx-users] calculation time

Dear users, Sometimes, in the end ( in production simulation), Gromacs doesn't show calculation/finish time on screen, why? How can we show it? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] calculation time

: Wednesday, 19 October 2011 3:08 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] calculation time On 19/10/2011 5:26 AM, ahmet yıldırım wrote: Dear users, Sometimes, in the end ( in production simulation), Gromacs doesn't show calculation/finish time on screen, why? How can

Re: [gmx-users] calculation time

, 3.0 ps. 2011/10/19 Mark Abraham mark.abra...@anu.edu.au On 19/10/2011 5:04 PM, ahmet yıldırım wrote: For example; grompp -f run.mdp -p topol.top -c pr.gro -n index.ndx -o run.tpr mdrun -v -deffnm run ... 1500 steps, 3.0 ps. step 100, will finish Sun Nov 27 19:11:00 2011

[gmx-users] gromacs synaptic package manager

Hi, I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 Synaptic Package Manager. What else should I do? I want to run a simulation in parallel on a single PC. Which commands should I enter the terminal? Thanks a lot for any instruction. -- gmx-users mailing list

Re: [gmx-users] gromacs synaptic package manager

/gromacs-4.5.1/include' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' make: *** [install-recursive] Error 1 2010/10/1 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Hi, I've installed GROMACS 4.0.3 and MPI libraries using

Re: [gmx-users] gromacs synaptic package manager

by running: sudo make install or rerun the installation steps with ./configure --prefix=$HOME/usr to install it in your home directory. Roland 2010/10/1 ahmet yıldırım ahmedo...@gmail.com Dear justin, Thanks for your reply. I did that you said. I tried to install Gromacs 4.5.1but I failed

Re: [gmx-users] gromacs synaptic package manager

not found -h The program 'pdb2gmx' is currently not installed. You can install it by typing: sudo apt-get install gromacs bash: pdb2gmx: command not found 02 Ekim 2010 02:08 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear Roland, Eventually I installed

[gmx-users] resolved pdm2gmx

Hi, I've written the Gromacs Mail list before, but I did not get the answer that I wanted. I am new user Gromacs. *1. I installed fftw-3.2.2 as following* a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure

Re: [gmx-users] resolved pdm2gmx

...@anu.edu.au - Original Message - From: ahmet yıldırım ahmedo...@gmail.com Date: Monday, October 4, 2010 18:41 Subject: [gmx-users] resolved pdm2gmx To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, I've written the Gromacs Mail list before, but I did not get

[gmx-users] published paper related to protein simulation using gromacs

Dear Gromacs users, I am new user Gromacs. I want to study on protein simulation using gromacs. If possible, Can you send a few articles on the protein simulation using Gromacs?For example, I downloaded from Protein Data Base the PDB extension file of any protein. What is the purpose of protein

[gmx-users] DSSP error

Hi, I installed in /usr/local/bin the DSSP program. And I set the environment variable with a command such as “export DSSP=/usr/local/bin/dssp”. a...@ubuntu:/Desktop/work# do_dssp -s run.tpr -f run.xtc ... Selected 1: 'Protein' There are 164 residues in your selected group Opening library file

Re: [gmx-users] DSSP error

-- *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [ahmedo...@gmail.com] *Sent:* Wednesday, November 10, 2010 10:02 PM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] DSSP error Hi, I installed in /usr/local

Re: [gmx-users] DSSP error

Dear Justin, Thanks for your replies a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb bash: /usr/local/bin/dssp: cannot execute binary file 2010/11/10 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: Dear Justin, I don't undertand you said you haven't chmod +x dssp)? Please

Re: [gmx-users] DSSP error

1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp 4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=/usr/local/bin/dssp Dear Justin, I compiled the

Re: [gmx-users] DSSP error

10.000 100% gcq#29: No One Could Foresee the End That Came So Fast (Slayer) 2010/11/10 Justin A. Lemkul jalem...@vt.edu ahmet yıldırım wrote: 1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC 3.step-r...@ab

Re: [gmx-users] DSSP error

I do not have any problem. The problem is solved. Thank you very much 10 Kasım 2010 22:45 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear Justin, Finally, The problem is solved, Thank you very much for your patience. Ps: I set *r...@ab-desktop:/home/ab

[gmx-users] water model purpose?

Hi, pdb2gmx -f 1LYD.pdb -water tip3p Why is -water tip3p command ( tip3p water model) used? What the purpose? Afterwards, genbox command is already added to solvent water as the following: genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro Thanks -- Ahmet YILDIRIM --

[gmx-users] RMSD and Resolution

Hi, Is there a relationship between RMSD value obtained from the calculation and Resolution value in PDB file? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

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