Re: [gmx-users] Hydrogens missing during parameterization

are not explicitly described! On Apr 14, 2010, at 12:05 PM, Anirban Ghosh wrote: Hi, XAvier, Sorry for that mistake. Yes, exactly PRODRG is not giving the non-polar hydrogens. There I am using the GROMOS96.1 FF. So is there any way to get the proper .itp file? I mean any other online server like

[gmx-users] Joining two peptide chains

Hi ALL, Is there any way in GROMACS to join two peptide chains by forming a peptide bond between the C and N atoms? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Joining two peptide chains

Hi ALL, Is there any way in GROMACS to join two peptide chains by forming a peptide bond between the C and N atoms? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Hydrogen Bond Acceptor-Donor List

Hi ALL, Is there any way in GROMACS to get the residue list (acceptor-donor list) for an entire simulation? Using g_hbond we get the number of h-bonds at every frames. But I want to get the list of residue pairs forming those hbonds at every frame. Any suggestion is welcome. Thanks a lot in

[gmx-users] Free Energy Calculation

Hi ALL, I have run a protein + ligand simulation using GROMACS4.0.7. I want to do a free energy calculation now. However, in my mdrun option I did not use the -dgdl option, nor I have used free_energy=yes in the MDP file (as I was not sure that I will be calculating free energy later). How can I

[gmx-users] Free Energy Calculation

Hi ALL, I have run a protein + ligand simulation using GROMACS4.0.7. I want to do a free energy calculation now. However, in my mdrun option I did not use the -dgdl option, nor I have used free_energy=yes in the MDP file (as I was not sure that I will be calculating free energy later). How can I

[gmx-users] Finding H-Bond donor-acceptor pairs

Hi ALL, I was just wondering if GROMACS has any tool to list out the hydrogen bond donor-acceptor pairs (in terms of residue names/numbers) throughout a MD simulation, say 10 ns. Can g_hbond be used to do this or is there any other command/method? Any suggestion is welcome. Regards, Anirban --

Re: [gmx-users] trjcat error

:49 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Anirban, Check each trajectory with gmxcheck to see whether they are okay. Cheers, Tsjerk On Fri, Dec 18, 2009 at 7:32 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I have 3 5 nano-seconds trajectory files (.trr

Re: [gmx-users] trjcat error

:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Anirban Ghosh wrote: Thanx Tsjerk for the reply. I checked the .trr files with gmxcheck and one of the .trr files is giving the error

[gmx-users] trjcat error

Hi ALL, I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water simulation. I am using trjcat to join them into a single .trr file for analysis and getting the following error:

[gmx-users] Topology file error for a ligand

Hi ALL, I want to do a simulation of a protein in presence of a ligand (L-DOPA). I am trying to obtain the topology of L-DOPA from the PRODRG server. However I am getting an error in the number of atoms in the PDB file (with all hydrogens) and the topology parameter file. The PDB file consists of

[gmx-users] Solvating a CG system

Hi ALL, I have a CG protein in a CG lipid bilayer. I have packed the lipids around the protein using InflateGRO, following Justin's tutorial. Now I want to solvate it with CG waters. In all-atom we need to set a higher value for VanderWaal's radii for C in vdwradii.dat file. What should it be

[gmx-users] Problem with CGMD

Hi ALL, Thanks Justin for your reply. Now after solvating my CG system of protein in lipid bilayer, I did EM and the final energy values were reasonable. But while running MD I am getting the following error: ---

Re: [gmx-users] Problem with CGMD

30, 2009 at 7:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Thanks Justin for your reply. Now after solvating my CG system of protein in lipid bilayer, I did EM and the final energy values were reasonable. But while running MD I am getting the following error

[gmx-users] Aligning protein in bilayer with editconf

Hi ALL, I am facing a strange problem, while aligning a protein molecule in a lipid bilayer. I am using the center coordinates of the lipid .gro file (values in the last line of .gro) with -box option of editconf to properly align the protein with the bilayer. Now the problem is that the protein

[gmx-users] Hg2+ ions in ion.itp

Hi ALL, My protein system contains Hg ions. As a result GROMACS4.0.5 is throwing the error Fatal error: Residue 'HG' not found in residue topology database How to solve tis issue? Can I add required parameters in the ions.itp file? If so can someone kindly provide the required parameters for

[gmx-users] GridMat MD Plot

Hi ALL, I ran a membrane simulation and for analysis I came across the GridMat MD software. However I am not able to plot the output values (Z values of a 20x20 matrix) as given in http://bevanlab.biochem.vt.edu/GridMAT-MD/examples.html . In my system Xmatrix is not working and I am trying to

[gmx-users] Re: GridMat MD Plot (Justin A. Lemkul)

Hi Justin, Thanks a lot Justin. It has solved my problem. Bye,  Anirban GhoshGrade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Looking for local information? Find it on Yahoo! Local

[gmx-users] GridMatMD Result Interpretation

Hello Justin, I have a query regarding the interpretation of the results of GridMatMD. In your paper you have given the eg. of KALP-DPPC simulation. The colour index (blue to red) ranges from 2.5 to 4.5. Its the distance between the P atoms of DPPC in the top and bottom layers i.e. the Z

[gmx-users] make_ndx option

Hi ALL, I want to create an index file using make_ndx which will contain only C-alpha atoms of some residues (like from residue no 2-10, res 25-30, res 36-40). How should I give this option in make_ndx. Any suggestion is welcome. Regards,  Anirban GhoshGrade Based Engineer Bioinformatics

[gmx-users] Simulation Temperature for GPCR in POPC bilayer

Hi ALL, Thanks a lot for your replies regarding extending water box. I could finally solve the problem by first removing the periodicity from the original POPC pdb files and then properly using editconf with -box option. In Justin's tutorial on setting up a membrane simulation, the temperature

[gmx-users] Re: Extending water in negative Z direction

Hi ALL, Thanks for the reply. I think what I mean will be more clear by just having a look at the structure (attached). I have tried by increasing the Z value, as suggested by David, but that only extends the water on one side of the bilayer only and not on the other side (which I need).

[gmx-users] Entending water in negative Z direction

coordinate value of the last line of the .gro file I am able to extend the water layer in the positive Z direction. But I am not able to extend it in the opposite direction. Decreasing the Z coordinate value is not helping that. How to do this? Any suggestion is welcome. Regards,  Anirban Ghosh

[gmx-users] Re: Extend water layer along negative Z-direction

Hi ALL, Thanks a lot Chris, Justin and Tsjerk for yor replies. Actually, my problem is not fully resolved. A portion of the protein tail is outside the water box in the Z direction (coordinate in Z is -35). So as suggested by you when I am issuing the command editconf -f box.gro -o BOX.gro

[gmx-users] Extend water layer along negative Z-direction

Hi ALL, I have a system of a GPCR protein in a lipid bilayer. I want to extend the water layer along the negative Z-direction. I found a script by Chris at the GROMACS mail list. But I am unable to use it properly. Can anyone please explain how to use it to extend the water layer only in the

[gmx-users] Error for 1-4 interaction

Hi ALL, I am following Justin's tutorial to run a protein in POPC bilayer simulation. However while doing a NVT simulation (after EM) I am getting the following error: step 0Warning: 1-4 interaction between 817 and 822 at distance 3.275 which is larger than the 1-4 table size 2.200 nm I

[gmx-users] RE: Lipids forming unsual bonds

Hi Dallas, Mark Chris, Thanks a lot for your replies. Yes, the problem was due to visualization artifacts and was solved by using the dynamic bonds representation of VMD. Thanks a lot. Regards,  Anirban GhoshGrade Based Engineer Bioinformatics Team Centre for Development of Advanced

[gmx-users] Lipids forming unsual bonds

Hi ALL, I am simulating a GPCR protein in a POPC bilayer. I have followed Justins' tutorial to set up the system, but have used POPC instead of DPPC. I have used the same parameters given in that tutorial. Till equilibration everything went well. But after releasing the protein in the

[gmx-users] How to remove water from lipid bilayer core

Hi ALL, I have a built a system of protein embeded in lipid bilayer and solvated it according to the GROMACS membrane simulation tutorial. I want to delete a few water molecules that are there in the hydrophobic core of the bilayer. I deleted them manually from the .gro file and corrected the

[gmx-users] Re: Problem with protein in lipid bilayer simulation

Hello Pawan and Justin, Thanks for the reply. I have removed the HW entries from the ffG53a6nb_lipid.itp file and still getting the error: -- Fatal error: Unknown atomtype OW

[gmx-users] Re: Problem with protein in lipid bilayer simulation

Hello Justin, Thanks a lot for the reply. Your tutorial is indeed very good. I followed your tutorial on protein-lipid simulation. I added the non-bonded parameters from the lipid.itp file to the ffG53a6nb_lipid.itp file. You have told to either delete the atom-type HW entries having zero values

[gmx-users] Atom -C not found in residue MET1 while adding hydrogens

Hi ALL, I have a protein pdb file generated using MODELLER. When I use the pdb2gmx command on it, it throws the error: Atom -C not found in residue MET1 while adding hydrogens and Atom OXT in residue LEU 404 The initial and end of the pdb file is like this:

[gmx-users] Replacement for G43b1 force field?

? The new manual for GROMACS4.0 also does not reflect this change. Any suggestion is welcome. Regards, Anirban Ghosh Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Bollywood news, movie reviews, film trailers and more! Go to http

[gmx-users] How to build a lipid bilayer in GROMACS?

, Anirban Ghosh Grade Based Engineer Bioinformatics Team Scientific Engineering Computing Group Centre for Development of Advanced Computing Pune, India Anirban Ghosh Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune, India Now surf

[gmx-users] g_covar Segmentation fault

the group consisting the entire system, for least square fit and covariance analysis, it is giving Segmentation Fault. Am I doing anything wrong. Any suggestion is welcome. Regards, Anirban Ghosh Grade Based Engineer Bioinformatics Team Centre for Development of Advanced Computing (C-DAC) Pune

[gmx-users] Re: gmx-users Digest, Vol 60, Issue 89

-- I also edited the aminoacids.dat file by giving the CG Beads names there. Do I need to incorporate any other change? Regards, Anirban Ghosh Grade Based

[gmx-users] FFTW problem for Gromacs4

suggestion is welcome. Regards, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Implicit solvent PBC

Hi All, I am simulating a Coarse Grained model using implicit solvent condition. Can Periodic Boundary Condition and Particle-Mesh-Ewald be used with implicit solvent simulation? Thanks, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Unlimited freedom, unlimited

[gmx-users] How to run on MARTINI Force Field in GROMACS

it? Regards,     Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Did you know? You can CHAT without downloading messenger. Go to http://in.webmessenger.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] How to do CGMD in GROMACS?

Hi All, I am interested in doing Coarse Grained MD in GROMACS. Is there any module in GROMACS with which I can do this? Please tell me the procedure of doing CGMD in GROMACS. Thanks a lot. Regards,   Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Explore your hobbies

[gmx-users] Calculation of Dihedral angles

on dihedrals. Select -d Or should I use g_dih? Please let me know how to use these. Thanks. Regards, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Project Trainee Centre For DNA Fingerprinting Diagnostics (CDFD) Hyderabad India - Get

[gmx-users] How to take snapshots every 1 nano-sec of a 30 nano-se simulation?

Hi All, Can anyone tell me how to take snapshots every 1 nano-sec of a 30 nano-se simulation? Which command should I use in GROMACS and how? Any suggestion is welcome. Thanks Regards, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Project Trainee Centre For DNA

[gmx-users] What Parameters Can Be Analyzes Using Data of .edo File?

. Regards, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Project Trainee Centre For DNA Fingerprinting Diagnostics (CDFD) Hyderabad India - 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here

[gmx-users] How to use .edo file to get information?

Hi All, While doing ED sampling along first eigen vector, I am generating a .edo file as output. How do I use this edo file to get relevant information? Any suggestion is welcome. Thanks. Cheers, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Project Trainee Centre

[gmx-users] How to define simulation time in mdp file?

rcoulomb = 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel= no Any suggestion is welcome. Regards, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Hyderabad - 500 046 Andhra Pradesh India

[gmx-users] Doubt about -linfix, -linacc, -radfix, -radacc, -radcon

does fixed step linear expansion and fixed step radius expansion specify here? How should I give the string options for these algorithms and which one should I use? I shall be glad if you can briefly explain the meaning of these algorithms. Looking forward to your replying. Regards, Anirban

[gmx-users] How to visualize .edo file

Hi All, I have generated a .edo file through mdrun and now want to analyze it. Can anyone tell me how to visualize/analyze this .edo file. All suggestions are welcome. Regards, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Hyderabad - 500 046 Andhra Pradesh India

[gmx-users] make_edi command options

to be given after -linfix as the string. What does this string specify? All suggestions are welcome. Regards, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Hyderabad - 500 046 Andhra Pradesh India - Why delete messages? Unlimited

[gmx-users] Re: gmx-users Digest, Vol 41, Issue 15

Hi All, I actually want to do the analysis in a particular direction of motion i.e. along first principle component, thats why i am trying to run the make_edi command, to get the desired direction component. Please suggest how to proceed to achieve this type of analysis. Regards, Anirban

[gmx-users] How to run ED with position restrain along first principle component

Hi All, I want to do essential dynamics study with position restrain along first principle component. But I don't know how to proceed. Is there any command in GROMACS to do is? Or do I need to manually create any file for doing this? Please tell me how to do this. Regards, Anirban Ghosh

[gmx-users] Hessian Matrix Doubt

option in GROMACS? Please suggest. Regards, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Hyderabad - 500 046 Andhra Pradesh India - Unlimited freedom, unlimited storage. Get it now___

[gmx-users] How to proceed with energy minimization for Normal Mode Analysis

to get a well minimized structure in order to go for Normal mode Analysis? Please suggest any protocol. Regards, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Hyderabad - 500 046 Andhra Pradesh India

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