Re: [gmx-users] Position restraints

On 16/06/2011 11:54 AM, Tom Dupree wrote: Greetings all, I have run into a little bit of a problem. I am trying to simulate a hetro-dimer. Through previous work we have identified 302 C-alphas (of 960 odd residues) that don't move much. Previously we position restrained these atoms in our si

[gmx-users] RE: Including quadrupole-charge interaction in GROMACS (WU Yanbin)

Hi, Not implemented in Gromacs AFAIK. Note that (1) even the definition of a quadruple isn't straightforwards and depends on the orientation and (2) common FF parameters were not developed with higher ordered multiple taken into account. @Article{Plattner2009, author = "Plattner, N and Meuwly, M

Re: [gmx-users] Including quadrupole-charge interaction in GROMACS

Quadrupole interactions are implicit whenever you have a molecule withe more than two partial charges. You don't have to include it explicitly. There are, however, multipole expansion techniques to speed up electrostatics calculations, but that's another story. Erik 15 jun 2011 kl. 23.45 skrev

[gmx-users] Implicit solvent calculatiom

Hi, My system is protein +DNA. I am trying to perform implicit solvent calculation using Amber 99. In the begging I wanted to minimize the system and got this error message. GB parameter(s) missing or negative for atom type 'OS' GB parameter(s) missing or negative for atom type 'H2' GB paramete

[gmx-users] Position restraints with multiple identical molecules

Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined -DPOSRES in the .mdp

Re: [gmx-users] Position restraints with multiple identical molecules

Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply a position restraint to the 91st atom of each molecules. Since all my molecules are identical I only have one [moleculetype] which contains 91 atoms. I have defined

[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97

Dear Sir, I found an error which is given below as i run grompp for position-restraint Fatal error: Group DRG not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. The error was attempted with -n b

Re: [gmx-users] Group DRG not found in indexfile

Please choose an informative subject line, especially when initiating a new thread. ITHAYARAJA wrote: Dear Sir, I found an error which is given below as i run grompp for position-restraint Fatal error: Group DRG not found in indexfile. Maybe you have non-default goups in your mdp file, whi

Re: [gmx-users] Position restraints with multiple identical molecules

You already are. The [position_restraints] directive is applied to the atom(s) of the [moleculetype] that >contains it, so if you only have one [moleculetype] then any instance of it will have the restraint >applied to whatever atoms are indicated. -Justin Hi Justin, thanks for your reply.

[gmx-users] an error for .tpr files

Hi all I want to run a program in a Quad Core PC and in cluster. the program was run succesfuly in my PC but when I run it in cluster I have the following error. Would you please help me? Can not open file: topol.tpr the .tpr file "filename.tpr" that I want run it is in my folder. Thanks alot

[gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA

Hi I had a simulation run with 4.0.7, using opls-aa for a protein in water. I now use part of the protein coordinates output from the simulation, and use pdb2gmx as: pdb2gmx -f conf.gro -ff oplsaa -ignh pdb2gmx complains that it cannot find HISB. I checked that the topology files in 4.5.3 do no

Re: [gmx-users] Position restraints with multiple identical molecules

Hi Justin, Ok - the .tpr file only lists the atoms from the molecule type. I get it now. Thanks again! Craig On 16 Jun 2011, at 12:58, Justin A. Lemkul wrote: Craig Kitchen wrote: Dear All, My system consists of 32 identical molecules (with 91 atoms per molecule). I would like to apply

Re: [gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA

On 16/06/2011 11:01 PM, maria goranovic wrote: Hi I had a simulation run with 4.0.7, using opls-aa for a protein in water. I now use part of the protein coordinates output from the simulation, and use pdb2gmx as: pdb2gmx -f conf.gro -ff oplsaa -ignh pdb2gmx complains that it cannot find HIS

Re: [gmx-users] an error for .tpr files

On 16/06/2011 10:35 PM, Maria Hamilton wrote: Hi all I want to run a program in a Quad Core PC and in cluster. the program was run succesfuly in my PC but when I run it in cluster I have the following error. Would you please help me? Can not open file: topol.tpr the .tpr file "filename.tpr" th

Re: [gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA

thought of that, but the trajectory also has HISB data .. so I guess I will have to alter it frame by frame ? On Thu, Jun 16, 2011 at 4:32 PM, Mark Abraham wrote: > On 16/06/2011 11:01 PM, maria goranovic wrote: > >> Hi >> >> I had a simulation run with 4.0.7, using opls-aa for a protein in water

Re: [gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA

On 17/06/2011 12:33 AM, maria goranovic wrote: thought of that, but the trajectory also has HISB data .. .xtc and .trr trajectories have no atom identification. That's why lots of the tools require a .tpr or coordinate file, together with a trajectory file in order to function. Using bash, lo

Re: [gmx-users] Including quadrupole-charge interaction in GROMACS

Hi, Erik, Thanks for the information. Regarding using more than two partial charges to mimic quadrupole explicitly, is there a one-to-one relation between the quadrupole moments and "position and magnitude" of the partial charges? For example, if I would like to include quadrupole moment for carb

[gmx-users] g_dist

Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I want to calculate how many CL atoms are in cutoff distance relative to hydorgen aotm of cation. I considered all CL atoms are distinguishable. Basically I want to calcualte the distance between each CL atom and correponing hyd

Re: [gmx-users] Including quadrupole-charge interaction in GROMACS

Hi, For neutral species, I think it's straightforward (unless the paper Ran Friedman mentioned says otherwise). Just use the definition of the quadrupole moment to figure out where to put the charges and what magnitude to assign to them. The electric field from a quadrupole declines like r^-3,

[gmx-users] g_hbond

Hi, I am little confused about setting up the two groups in g_hbond. 1. Are the two groups corresponding to the donor (N) and the acceptor (O) atoms? I want to measure the lifetime, angle and distance of the triplet N-HO hydrogen bond. Is this the triplet that the manual talks about? Thanks

[gmx-users] g_dist

Dear Nilesh: You don't seem to have made any progress since Mark gave you some reading hints. Your best chance to get a useful response follows the general form: 1. I want to do A. 2. I tried method B, here are the exact commands that I used (copy and paste) 3. With that method, I obtain C

[gmx-users] Can't unfold the protein

Hi, I have question about unfolding. I use three different ways respectively but all failed. The three way is, 1. 600K in 20ns, then the system explode. 2. 400K in 10ns, the protein is very stable and the value is almost the same in radius of gyration. 3. heating up from 300K to 400K in 2ns and

[gmx-users] Can't unfold the protein

Dear Hsin-Lin: The first thing that comes to mind is using very high temperatures with NVT. Obtaining the desired denatured state is a complex challenge, but you might try this paper: Phys. Rev. Lett. 93, 238105 (2004) Reversible Temperature and Pressure Denaturation of a Protein Fragment:

Re: [gmx-users] Implicit solvent calculatiom

On 16/06/2011 7:59 PM, Netaly Khazanov wrote: Hi, My system is protein +DNA. I am trying to perform implicit solvent calculation using Amber 99. In the begging I wanted to minimize the system and got this error message. GB parameter(s) missing or negative for atom type 'OS' GB parameter(s) mis

[gmx-users] Can't unfold the protein

Dear Chris, Thank you for your reply. My protein is very stable. I simulated it in 300ns in 300K before but there was almost no change. That's why I want to do denaturation now. I want to start a new simulation on the protein which is unfolded. And I'll read the paper you told me. Thank you.

[gmx-users] Gromacs to Amber trajectory

Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory f

[gmx-users] Can't unfold the protein

Dear Hsin-Lin: I am no expert in this area. I am just saying that if you get densities that are way too low in NPT, then you might alleviate this problem with NVT. In fact, I would personally do this in vacuum without pbc and use the sd integrator. Then you can sample extended conformatio

[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

Hi, everyone: I am a new user of Gromacs, and I am running through the tutorial. When I am trying to run the ligand-receptor binding tutorial from http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html I met some trouble in adding ion. Each

Re: [gmx-users] Can't unfold the protein

Hey, NPT is not the appropriate way to do this kind of simulations. I am not sure whether or not the water models available for classic MD simulations are able to reproduce the phase behavior. Indeed what you see when your system explodes and gets huge is the water evaporating. What is gene

[gmx-users] Heat Capacity Question

Hello, I am trying to compare the heat capacity (at NPT) of 1000 molecules of methanol. I ran it all to equilibrium and used g_energy and -nmol 1000 to calculate the heat capacity. The value I achieved, ~140 J/mol*K is far from what I see is 79.5 J/mol. I have read on some past posts that there

[gmx-users] Including a solvation model after converting from AMBER to GROMACS

Hello, I first used Antechamber and Leap to generate the topology and coordinate files for benzamide.pdb. I then converted them to gromacs formats and added the water molecules using the following commands: editconf -f benz.gro -bt dodecahedron -d 1.2 -o benz_box.gro genbox -cp benz_box.gro -cs

[gmx-users]gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

> Hi, everyone: > I am a new user of Gromacs, and I am running through the tutorial. > When I am trying to run the ligand-receptor binding tutorial from > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html > I met some trouble in adding ion.

[gmx-users] g_hbond

Hi, To help clarify my previous g_hbond question, I have these two groups in my index file [ a_100_a_101]  # 100 is N, #101 is H    100 101 [ a_200 ]    # 200 is O    200 when I ran g_hbond, I got "Found 1 donors and 2 acceptors". The part that I don't quite understand is why it

[gmx-users] g_hbond

From g_hbond -h "OH and NH groups are regarded as donors, O is an acceptor always, N is an acceptor by default, but this can be switched using -nitacc. Dummy hydrogen atoms are assumed to be connected to the first preceding non-hydrogen atom." The two groups are to find hbonds between gro

[gmx-users] Re: Gromacs error

Hi, I have installed gromacs 4.5 on fedora core 15 and whenever I try to run any command like pdb2gmx ... I am getting the following error : error while loading shared libraries: libgmx.so.6: cannot enable executable stack as shared object requires: Permission denied Pls help?? -- Bharat --

RE: [gmx-users] Re: Gromacs error

Someone with some more in depth knowledge will hopefully pipe up, but until then there are some things you can read up on and see if it will solve your issue. Google is your friend. Put "error while loading shared libraries: libgmx.so.6: Permission denied" into it, and you get a number of top

Re: [gmx-users] Gromacs to Amber trajectory

On 17/06/2011 2:57 AM, Raja Pandian wrote: Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package

Re: [gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

Ye Yang wrote: Hi, everyone: I am a new user of Gromacs, and I am running through the tutorial. When I am trying to run the ligand-receptor binding tutorial from http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html I met some troubl

Re: [gmx-users] Re: Gromacs error

thanks.. I fixed the problem by using the command execstack -c filename but I have another issue .. I am am preparing the structure for simulation which is a docked complex containing Phospharylated tyrosine. I am using Amber 99 force field and update the residuetypes.dat, aminoacid.rtp, ffbonde

[gmx-users] load imbalance

Hi all, I am trying to run GB model simulation of a small protein. I keep getting these errors for every step printed to the log file. DD load balancing is limited by minimum cell size in dimension X DD step 35999 vol min/aver 0.799! load imb.: force 154.9% Below i copied my mdp parameters. I

Re: [gmx-users] load imbalance

On 17/06/2011 12:44 PM, E. Nihal Korkmaz wrote: Hi all, I am trying to run GB model simulation of a small protein. I keep getting these errors for every step printed to the log file. DD load balancing is limited by minimum cell size in dimension X DD step 35999 vol min/aver 0.799! load imb

[gmx-users] monitoring the water molecules

Hi gmx-users. I am doing MD simulation with the green fluorescent protein, where confined water molecules exist inside the protein barrel. During the coarse of the simulation i noticed these confined water molecule get exchange with outside bulk water. Is it possible to monitor or mark the wat

Re: [gmx-users] Gromacs to Amber trajectory

Dear All, I have created Amber input file (.prmtop and .rst7) using Xleap. And then I have converted this input file into Gromacs input file format (*.gro and *.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber Force Field). Now I would like to convert Gromacs trajectory f

Re: [gmx-users] monitoring the water molecules

On 17/06/2011 12:55 PM, Ramachandran G wrote: Hi gmx-users. I am doing MD simulation with the green fluorescent protein, where confined water molecules exist inside the protein barrel. During the coarse of the simulation i noticed these confined water molecule get exchange with outside bulk

[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97

Dear Sir, Above error was solved but the system has raised a following new error, i.e., Fatal error: 52 atoms are not part of any of the T-Coupling groups How do I find which atom file has problem? help me to solve this problem... -- ** Ithayaraja M, Research Scholar, Department of Bi

[gmx-users] Regarding H-bond autocorrelation

Thanks Sir,for your reply... I have a silly question regarding the g_hbond's autocorrelation output: The output contains the following four columns (i)  Ac fin sys(t) (ii)  Ac(t) (iii) Cc contact,hb(t) (iv) -dAc fs/dt As I understood the first column is the acf with background subtraction,and the

Re: [gmx-users] Re: gmx-users Digest, Vol 86, Issue 97

On 06/17/2011 02:53 PM, ITHAYARAJA wrote: Dear Sir, Please use a descriptive email subject line. Above error was solved but the system has raised a following new error, i.e., Fatal error: 52 atoms are not part of any of the T-Coupling groups How do I find which atom file has problem? Loo

[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97

On 17 June 2011 10:23, ITHAYARAJA wrote: > Dear Sir, > Above error was solved but the system has raised a following new error, > i.e., > > Fatal error: > 52 atoms are not part of any of the T-Coupling groups > > How do I find which atom file has problem? > help me to solve this problem.

[gmx-users] cross correlations

Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but that's not what i'm looking for. The result I want should be an NxN matrix wit

Re: [gmx-users] thermostats

On 06/17/2011 03:27 PM, ITHAYARAJA wrote: Use a descriptive subject line. On 17 June 2011 10:23, ITHAYARAJA > wrote: Dear Sir, Above error was solved but the system has raised a following new error, i.e., Fatal error: 52 atoms are not