Re: [gmx-users] Error in pdb2gmx

vivek sharma wrote: Hello there, I am trying to run pdb2gmx on 3bzu.pdb file and got the following error Opening library file /usr/share/gromacs/top/ ffG43b1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Reading 3bzu.pdb... WARNING: all CONECT records are ignored Read 'CORTICOST

[gmx-users] requested for GROMACS package

hello I am working with protien 1PGB having 56 amino acids (practical tutorial from GROMACS web site) for its simulation using the flexilbe water. the commands that i have run are : At later stsges of MD simulations ( i.e after position restrained MD), I have been getting few errors which are as f

Re: [gmx-users] requested for GROMACS package

shiny chandy wrote: hello I am working with protien 1PGB having 56 amino acids (practical tutorial from GROMACS web site) for its simulation using the flexilbe water. the commands that i have run are : At later stsges of MD simulations ( i.e after position restrained MD), I have been gettin

Re: [gmx-users] Error in pdb2gmx

Hi David, Thanks for the quick reply. My apologies for asking you again a silly doubt as, I am doing this all for the first time. It will be of great help if you can tell me how to do such correction manually. With Thanx, Vivek 2008/8/12 David van der Spoel <[EMAIL PROTECTED]> > vivek sharma wro

Re: [gmx-users] Error in pdb2gmx

vivek sharma wrote: Hi David, Thanks for the quick reply. My apologies for asking you again a silly doubt as, I am doing this all for the first time. It will be of great help if you can tell me how to do such correction manually. with a text editor, like emacs, notepad or whatever. With Tha

[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. .. .. .. ...

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. ..

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error.

[gmx-users] ASP-LIG Interaction Energy : MDRUN

Dear Gromacs Users,   I have just completed one (5ns ) mdrun.   Now If i want to calculate the interaction energy between two residues, my ligand and ASP104, how should I go about calculating the same.   The one option I know is by creating .ndx . But I did not expect this residue to play an imp

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel <[EMAIL PROTECTED]> > vivek sharma wrote: > >

Re: [gmx-users] Error in pdb2gmx

Hi david, Thanx again, but I want to ask what changes need to be done there in such cases. With Thanx, Vivek 2008/8/12 David van der Spoel <[EMAIL PROTECTED]> > vivek sharma wrote: > >> Hi David, >> Thanks for the quick reply. My apologies for asking you again a silly >> doubt as, I am doing thi

Re: [gmx-users] Error in pdb2gmx

vivek sharma wrote: Hi david, Thanx again, but I want to ask what changes need to be done there in such cases. The chain identifier needs to be continuous. That is, if you have atoms with chain identifiers like: A A B A C A A they should be re-written as: A A A A A B C This can be a

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

If atoms are missing in the sidechains of your protein, you can try a program like scwrl3 to rebuild all or some of the sidechains. This will give you complete sidechains in sort of reasonable positions. Cheers /Per 12 aug 2008 kl. 15.04 skrev vivek sharma: Hi David, Thanx a lot again.

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

Dear Vivek, you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs.   nahren --- On Tue, 8/1

Re: [gmx-users] ASP-LIG Interaction Energy : MDRUN

nahren manuel wrote: Dear Gromacs Users, I have just completed one (5ns ) mdrun. Now If i want to calculate the interaction energy between two residues, my ligand and ASP104, how should I go about calculating the same. The one option I know is by creating .ndx . But I did not expect this

Re: [gmx-users] pdb2gmx -inter automatised ?

Ok, "pdb2gmx < inter.txt" did the trick. Although it was a bit painful to generate the inter.txt in the first instance :) Thanks again Christian Fufezan Dr. Christian Fufezan Westfälische Wilhelms-Universität Münster Institut für Biochemie und Biotechnologie der Pflanzen (IBBP) Hinde

Re: [gmx-users] pdb2gmx -inter automatised ?

Hi :) Maybe these little scripts are useful... The first, titratable.sh (use: titratable.sh file.pdb), generates a list of residues for which the protonation state can be set, including the termini. The second, gmxquery.sh (use: titratable.sh file.pdb | gmxquery.sh) gives a series of 0 1 2, accor

[gmx-users] Re: requested for GROMACS package

> hello > I am working with protien 1PGB having 56 amino acids (practical tutorial > from GROMACS web site) for its simulation using the flexilbe water. > the commands that i have run are : > > At later stsges of MD simulations ( i.e after position restrained MD), I > have been getting few errors w

Re: [gmx-users] Error in pdb2gmx

Well, sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}' file.pdb | sort | cut -b 2- > sorted.pdb sort of seems to do the trick. But it will place the chainless things first. Hope it helps, Tsjerk On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

[gmx-users] one component plasma simulations (OCP)

hi, is it possible to do one component plasma (OCP) simulations using gromacs? in the one component plasma (OCP) charged particles immersed into a homogeneous neutralizing backround. so i would guess that the neutralizing backround is the difficult thing for gromacs i would appreciate very much

Re: [gmx-users] one component plasma simulations (OCP)

Argyrios Karatrantos wrote: hi, is it possible to do one component plasma (OCP) simulations using gromacs? in the one component plasma (OCP) charged particles immersed into a homogeneous neutralizing backround. so i would guess that the neutralizing backround is the difficult thing for gromacs

[gmx-users] gmx does not recognize HIE as protein

Hello, I am trying to simulate a protein that has 2 chains (in a membrane, but the problem is in the protein). One of the chains of the protein has 416 residues and the other 421. I want to simulate it using the amber force field, so I have prepared the topology for each one of them and then co

Re: [gmx-users] gmx does not recognize HIE as protein

Hi Rebeca, In the GMX data directory ($GMXDATA) there's a file aminoacids.dat listing what should be recognized as amino acids. Either edit the file and add HIE (also incrementing the counter at the top line) or make a local copy of the file in the directory where you need it and edit that. Cheer

[gmx-users] debian packages from CVS versions

Hi Folks, JFYI, I packaged the cvs version for deb based distributions (ubuntu, debian... ). I can provide source packages to build, update (from cvs) and install the current and probably future cvs versions on your machines. The packages should be installable together with 3.x packages since t

[gmx-users] error: 1 particles communicated to PME node 3 (...)

Hello, I am trying to equilibrate a protein+membrane system in Gromacs 4. The minimization went OK, but in the equilibration at constant pressure I got this error: Fatal error:1 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their ch

Re: [gmx-users] error: 1 particles communicated to PME node 3 (...)

Which version of CVS are you using? (This sounds like a question for the gmx-developers listserv.) I believe this problem was fixed in CVS over a month ago: http://www.gromacs.org/pipermail/gmx-developers/2008-July/002608.html Although there is a possibility that something is really wrong, wh

[gmx-users] Force Field Parameters Nitrogen and Oxygen

I am trying to simulate air and have not been able to find force field parameters for a Nitrogen Nitrogen bond or Oxygen Oxygen bond. If you could please direct me to where these could be found I would appreciate it. Thanks, Andy ___ gmx-users mailing l

[gmx-users] OCP simulations

hi David A one-component plasma (OCP) is a system in which a single species of charged particle moves in a uniform backround of the opposite charge.  Systems of this nature exist in the dense stellar matter of white-dwarf stars. when the screening parameter of the screened Coulomb goes to zero t

Re: [gmx-users] Force Field Parameters Nitrogen and Oxygen

Andy Shelley wrote: I am trying to simulate air and have not been able to find force field parameters for a Nitrogen Nitrogen bond or Oxygen Oxygen bond. If you could please direct me to where these could be found I would appreciate it. I believe these values typically come from spectrosc

Re: [gmx-users] Re: requested for GROMACS package

Vitaly Chaban wrote: P.S. Justin is extremely strict today. :) Apologies if I've been coming of a bit dry or sarcastic. I do try to help, at least by pointing individuals to the proper resources. We seem to be getting the same questions day after day :) I myself have received quite a

[gmx-users] A bug of trjconv for force output?

Hello All, I just found a strange problem for the gromacs tool trjconv. I have a trajectory (and the tpr file) which contains three groups of molecules and x,v and f. When I use trjconv to output the trajectory of the 1st group, everything is fine. For example, I have A,B and C groups in my tra

[gmx-users] colour of the molecules

Dear all gmx-users and developers, There are 6 different type of molecules in my simulation system. So how can I differentiate o recognize the type of those molecules? which files (topology, trr or others) should I look at? Any suggestions are appreciated. Thanks

Re: [gmx-users] Error in pdb2gmx

Thanx David and Tsjerk, I tried the option given by Tsjerk on pdb file, then pdb2gmx command on sorted pdb file was giving the following error. Sorting it all out... Opening library file /usr/share/gromacs/top/ffG43a1.hdb Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb Opening library

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

Hi Nahren, Thanx for your help, I opened the pdb file with swisspdb viewer and then tried the pdb2gmx command over that pdb file and got the following error. Total mass 28295.072 a.m.u. Total charge 1.000 e Writing topology Processing chain 5 'E' (372 atoms, 9 residues) There are 0 donors and 0 ac

Re: [gmx-users] Error in pdb2gmx

Hi Vivek, Sorry, I should've been more careful. Sorting will obviously take the rest of the line in account. I'll send a proper solution in a few moments... Cheers, Tsjerk On Wed, Aug 13, 2008 at 7:33 AM, vivek sharma <[EMAIL PROTECTED]> wrote: > Thanx David and Tsjerk, > I tried the option g

Re: [gmx-users] Error in pdb2gmx

Hi Vivek, I downloaded 3bzu.pdb and ran the sorting on it as I described before (sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}' 3bzu.pdb | sort | cut -b 2-), and it worked perfectly for me. I don't see how you'd end up with some atoms inbetween other residues. It seems as

Re: [gmx-users] colour of the molecules

Hi, On Wednesday, 13. August 2008, huan wrote: > Dear all gmx-users and developers, > > There are 6 different type of molecules in my simulation system. So how can > I differentiate o recognize the type of those molecules? which files > (topology, trr or others) should I look at? > > Any sugg

[gmx-users] Re: Force Field Parameters Nitrogen and Oxygen

> Date: Tue, 12 Aug 2008 16:36:16 -0500 > From: "Andy Shelley" <[EMAIL PROTECTED]> > Subject: [gmx-users] Force Field Parameters Nitrogen and Oxygen > To: gmx-users@gromacs.org > Message-ID: ><[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > I am trying to simulate ai