Re: [gmx-users] NEUTRALISED CHARGES

Hi, You should add 14 cl ions. Regards, Pawan On Mon, Apr 6, 2009 at 12:26 PM, akalabya bissoyi < bissoyi.akala...@gmail.com> wrote: > hello gromacs > i am trying to minimise my protein-ligand complex in gromacs.but it shows > that system has non zero charge > can any body says how much *cl ion

RE: [gmx-users] Doubt regarding membrane protein in POPC bilayer

Apparently the final mdrun has not worked successfully. It would be interesting to see what the system looks like after the position restraint mdrun. Andreas >>> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Pawan Kumar Sent: 06 April 2009 07:47

[gmx-users] dihedral potential structure

Hello gromacs users, I want to ask a simple thing, which nevertheless is not really clear to me, but it's sometimes too important. For instance, I have in my molecule torsional angle around a double bond: -C-C(H)=C(H)-C-. The dihedral potential contains following four parts: -C-C=C-C-, a U1 from t

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. Thanks for your reply. After the position restraint mdrun the system looked quite justified as I restrained both the protein and the lipids. Is it because of the lesser number of steps ? I use 5000 steps with dt value of 0.002. Thanking you, Pawan On Mon, Apr

[gmx-users] human readable topology parameters in a top file?

Hi there, I was wondering if Gromacs would have a command to parse a top or itp file and return a friendly human readable file describing all the forcefield parameters in a way (for those who knows Amber) that 'rdparm' does for a Amber prmtop file. Many thanks in advance, Alan -- Alan Wilter S

RE: [gmx-users] Doubt regarding membrane protein in POPC bilayer

There is nothing wrong with the number of steps and the step size of 2 fs. Can you attach/send the coordinates of your system after position restraint MD ? What about your bilayer before inserting the protein ? Does it move apart during MD ? Definetly you should perform another position restra

Re: [gmx-users] human readable topology parameters in a top file?

Alan wrote: Hi there, I was wondering if Gromacs would have a command to parse a top or itp file and return a friendly human readable file describing all the forcefield parameters in a way (for those who knows Amber) that 'rdparm' does for a Amber prmtop file. No, there's no such tool. There a

Re: [gmx-users] editconf 2 warning

Homa Azizian wrote: Hi These 2 warning appeared after I did editconf for Drug-Protein Complex. WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type WARNING: vdwradii will be determined based on residue and atom nam

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. Before inserting the protein the bilayer was alright as I took the equilibrated bilayer from Dr. Tieleman's website. I have done the position restraint mdrun by restraining the protein only. In this case also the lipids pull apart. Thanking you, Pawan On Mon,

[gmx-users] Re: human readable topology parameters in a top file?

> I was wondering if Gromacs would have a command to parse a top or itp > file and return a friendly human readable file describing all the > forcefield parameters in a way (for those who knows Amber) that > 'rdparm' does for a Amber prmtop file. I do not know such command. However the topology f

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. Thanks for all your suggestions and help. The solvation is completed and the system is neutralized. The position restraint mdrun and final mdrun has worked out successfully without any warnings and errors this time. The structure after t

Re: [gmx-users] NEUTRALISED CHARGES

Pawan Kumar wrote: Hi, You should add 14 cl ions. Why 14? The number of Cl- ions that are necessary is pretty much spelled out by grompp, and the net charge of the system is printed in the .top (qtot section in [atoms]). If your system has a net charge of +2, add 2 Cl- ions, and so forth

Re: [gmx-users] dihedral potential structure

Филипп Орехов wrote: Hello gromacs users, I want to ask a simple thing, which nevertheless is not really clear to me, but it's sometimes too important. For instance, I have in my molecule torsional angle around a double bond: -C-C(H)=C(H)-C-. The dihedral potential contains following four part

Re: [gmx-users] NEUTRALISED CHARGES

There is a log attached in the first e-mail. My first reaction was the same. Why 14 :). Marius On Mon, Apr 6, 2009 at 1:10 PM, Justin A. Lemkul wrote: > > > Pawan Kumar wrote: > >> Hi, >> >> You should add 14 cl ions. >> > > Why 14? The number of Cl- ions that are necessary is pretty much spel

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. > 1. Were there gaps between the water and lipid headgroups? If so, the > lipids may be pulling towards the solvent. Restrain the lipids and run an > equilibration for a longer time. Gap was there when I used a value of 0.5 in the vdwradii.dat file. The

[gmx-users] RE: problem in pulling in gromacs 4.03

Other then to use 4.0.4, i would try to change the simulation-time, the force-constant of the spring (pull_k1) and the pulling velocity (pull_rate1). You have both a low force-constant and a slow pulling velocity, with a simulation-time around 500ps it is possible that only see the protein vibratin

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. 1. Were there gaps between the water and lipid headgroups? If so, the lipids may be pulling towards the solvent. Restrain the lipids and run an equilibration for a longer time. Gap was there when I used a value of 0.

Re: [gmx-users] NEUTRALISED CHARGES

Marius Retegan wrote: There is a log attached in the first e-mail. My first reaction was the same. Why 14 :). Ah, that would make sense. May I suggest a tip to all users: don't send attachments when it is just as simple to copy and paste text into an email. I often see small attachment fi

[gmx-users] solvent density around protein

First thanks Matt to reply me for my problem. As I say I want to calculate the density of solvent around protein. I already tried the commands g_density and g_densmap The g_density Compute partial densities across the box and g_densmap just give me one black and white photo which don't have sense.

[gmx-users] Grompp fatal error (Residue numbers in the .top are not numbered consecutively from 1)

Hi everybody, I am setting up an MD run on a peptide-protein complex with gromacs. I have defined the box and solvated the system, but now I'd like to equilibrate the solvent, so I tried with grompp, but an error occurs: Fatal error: Residue numbers in the .top are not numbered consecutively from

Re: [gmx-users] Grompp fatal error (Residue numbers in the .top are not numbered consecutively from 1)

annalisa bordogna wrote: Hi everybody, I am setting up an MD run on a peptide-protein complex with gromacs. I have defined the box and solvated the system, but now I'd like to equilibrate the solvent, so I tried with grompp, but an error occurs: Fatal error: Residue numbers in the .top are

Re: [gmx-users] Grompp fatal error (Residue numbers in the .top are not numbered consecutively from 1)

Hi, Justin, thank you for your reply. I have just checked my .itp files. I have 7 itp files: - one is generated by doing genpr to define the restraints on the protein; - six (two for each chain of my complex) are generated directly by pdb2gmx (first step of my simulation). The first itp file is ok

Re: [gmx-users] Grompp fatal error (Residue numbers in the .top are not numbered consecutively from 1)

annalisa bordogna wrote: Hi, Justin, thank you for your reply. I have just checked my .itp files. I have 7 itp files: - one is generated by doing genpr to define the restraints on the protein; - six (two for each chain of my complex) are generated directly by pdb2gmx (first step of my simulati

[gmx-users] partial charge on protein

Hi there is total charge of 0.08 on the protein, Is it correct to add 1 CL- or it should better ignore this? -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

Re: [gmx-users] Grompp fatal error (Residue numbers in the .top are not numbered consecutively from 1)

Thank you VERY VERY VERY much, Justin! I've done what you said and... Now it works!! Cheers! Annalisa - Annalisa Bordogna PhD. Student DISAT - Università degli Studi di Milano Bicocca Milano - Italy --

Re: [gmx-users] solvent density around protein

g_sorient spits out, at the end, among other things, the average number of solvent molecules within the cutoff distance. To get the number of e.g. water oxygens within a given distance of a group of atoms on a per frame basis, you can use g_hbond -contact. Best, Matt 2009/4/6 Morteza Khabiri :

Re: [gmx-users] partial charge on protein

Homa Azizian wrote: Hi there is total charge of 0.08 on the protein, Is it correct to add 1 CL- or it should better ignore this? You should absolutely NOT ignore this problem. You have a fractional charge of non-negligible magnitude. Did you use -missing with pdb2gmx? If so, you are pro

Re: [gmx-users] energy

Hi! Thanks for your mail. I used two different operating systems and in both I found this problem of the energy file recurring!! Well I will go ahead and use the tpdconv to extend the simulations. Thanks JJ On Sun, Apr 5, 2009 at 4:38 PM, Mark Abraham wrote: > jayant james wrote: > >> >> Hi! >> I

Re: [gmx-users] x2top & Encad all-atom force field (vacuum)

Dear All, I am resubmitting my question below as I did not receive a response and am thinking that my previous e-mail was not recognized by the system or missed. Could someone please provide me with an answer to my questions below? Many thanks. Darrell Koskinen On 4/2/2009, "" <> wrote: >>Date

Re: [gmx-users] x2top & Encad all-atom force field (vacuum)

darre...@ece.ubc.ca wrote: Dear All, I am resubmitting my question below as I did not receive a response and am thinking that my previous e-mail was not recognized by the system or missed. Could someone please provide me with an answer to my questions below? Many thanks. Darrell Koskinen On 4/

[gmx-users] partial charge on protein

Hi according to my problem about non-neglible magnitude partial charge on protein, I did not use -missing option with pdb2gmx my command is: pdb2gmx -ignh -f .pdb -o .pdb -water spce what should I do to neutralize this charge? Thank you in advance. -- Tehran University of Medical Sciences www.tu

Re: [gmx-users] partial charge on protein

Homa Azizian wrote: Hi according to my problem about non-neglible magnitude partial charge on protein, I did not use -missing option with pdb2gmx my command is: pdb2gmx -ignh -f .pdb -o .pdb -water spce what should I do to neutralize this charge? You should probably start over and check car

[gmx-users] obtaining a pdb after a simulation with ffamber

Dear users, I've been running a MD simulation on a protein using ffamber94 (from amber ports with gmx 3.3.1). After the run, I extracted and minimized an average structure. I then converted the lowest energy structure (.gro) from the minimization in a pdb file with trjconv, but turns out som

[gmx-users] too_low_temperature

Dear all, I have a solvent (SW-water 519 molecules) and solute (NMA-peptide) system, whereby I coupled both of them seperately to a heath bath (Berendson , t=0.1 ps). Both heat baths have different T's, Solvent T=300K and Solute T=500K. The strange thing is that the temperature (g_energy)

[gmx-users] A question regarding the xdr lib

Hello, I just compiled the xdr file lib that was recently released on the Gromacs website. I'm just wondering what's the meaning of "char *fn" in the xdrfile_???.h as in: /* This function returns the number of atoms in the xtc file in *natoms */ extern int read_xtc_natoms(char *fn,int *natoms

Re: [gmx-users] A question regarding the xdr lib

LuLanyuan wrote: Hello, I just compiled the xdr file lib that was recently released on the Gromacs website. I'm just wondering what's the meaning of "char *fn" in the xdrfile_???.h as in: /* This function returns the number of atoms in the xtc file in *natoms */ extern int read_xtc_natoms(c

Re: [gmx-users] obtaining a pdb after a simulation with ffamber

Serena Leone wrote: Dear users, I've been running a MD simulation on a protein using ffamber94 (from amber ports with gmx 3.3.1). After the run, I extracted and minimized an average structure. I then converted the lowest energy structure (.gro) from the minimization in a pdb file with trjco

Re: [gmx-users] too_low_temperature

Sang-Min Park wrote: Dear all, I have a solvent (SW-water 519 molecules) and solute (NMA-peptide) system, whereby I coupled both of them seperately to a heath bath (Berendson , t=0.1 ps). Both heat baths have different T's, Solvent T=300K and Solute T=500K. The strange thing is that the t

[gmx-users] missing interactions for the LJ-decoupled molecule during free energy in parallel but not serial

Hello, I am doing free energy calculations with gromacs 4.0.4. For the system I am using, I have reliable runs without any crashes when running in serial. When I run in parallel, I get stochastic crashes, that always have the same form (see below). Note that the "missing interactions" always

RE: [gmx-users] A question regarding the xdr lib

Thanks very much, David. Lanyuan > Date: Mon, 6 Apr 2009 22:56:43 +0200 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] A question regarding the xdr lib > > LuLanyuan wrote: > > Hello, > > I just compiled the xdr file lib that was recently released on the > >

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. Sorry for the inconvenience about the .mdp file. The mdp file used for the final run is * final.mdp file** *title = Protein in POPC bilayer cpp = /usr/bin/cpp constraints = all-bonds constraint-algorithm= Lincs integra

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. Sorry for the inconvenience about the .mdp file. The mdp file used for the final run is *_ final.mdp file_*_ _title = Protein in POPC bilayer cpp = /usr/bin/cpp constraints = all-bonds constraint-al

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Hello Sir, Can you please tell me how to couple ions with SOL ? Is there any command in gromacs to do that ? Thanking you, Pawan On Tue, Apr 7, 2009 at 9:44 AM, Mark Abraham wrote: > Pawan Kumar wrote: > >> Respected Sir, >> >> Greetings from Pawan. >> Sorry for the inconvenience about the .mdp

[gmx-users] partial charge on protein

Hi Justin and all when I do this command: pdb2gmx -ignh -f .pdb -o .pdb -water spce with OPLS force field. it seems that the protein has the charge of -3, while the ligand has the charge of 0.890 and finally it prints that the final charge is -2.11. I neutralized this charge with 2 NA+ so -0.11

[gmx-users] the reson for neutralizing the charge

Hi I have a basic question about the charge. why is it important to neutralize the charge of ligand-protein complex. Is it true by neutralizing the tatal charge of ligand-protein complex we prevent the electrostatic intraction of ligand and protein? Any suggestion would be appreciated. -- Teh

RE: [gmx-users] missing interactions for the LJ-decoupled molecule during free energy in parallel but not serial

Hi, I think this behavior is "expectable". The simplest explanation would be that some particles at the ends of the molecule only have LJ and no charge, I guess this is not the case. The more probable explanation is that your molecule extends when the LJ are turned off, since there are no inter