Re: [gmx-users] Docking with PyMol and using Gromacs

dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Gunnar Widtfeldt

[gmx-users] Docking with PyMol and using Gromacs

Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I

Re: [gmx-users] Problem with topolbuild

Thank you. I am new to Unix commands, so could you please explain a little more how I am to apply these bug fixes? Thanks On Mon, Nov 9, 2009 at 12:51 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Sun, November 8, 2009 at 5:31:30 PM, Gunnar Widtfeldt Reginsson regins...@gmail.com wrote

Re: [gmx-users] Problem with topolbuild

It works. Thank you so much. Regards, Gunnar W. On Mon, Nov 9, 2009 at 4:26 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Mon, November 9, 2009 at 8:14:29 AM, Gunnar Widtfeldt Reginsson regins...@gmail.com wrote: Thank you. I am new to Unix commands, so could you please explain a little

[gmx-users] topolbuild

Hi. I downloaded topolbuild1_2_1 from the GROMACS website. I run the command make -f Makefile.G4OsX and there were no error messages. When I then write topolbuild -h I get command not found Does anyone know what I am doing wrong? NB! I am running Mac OS 10.5 on a ppc G4 Thanks, -- gmx-users

Re: [gmx-users] topolbuild

Right, I keep forgetting about the path. I got it now. Thanks. On Sun, Nov 8, 2009 at 6:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: Gunnar Widtfeldt Reginsson wrote: Hi. I downloaded topolbuild1_2_1 from the GROMACS website. I run the command make -f Makefile.G4OsX and there were

[gmx-users] Problem with topolbuild

Hi. I have a small organic molecule that I processed with antechamber using the gaff forcefield and got a mol2 file. I want to get .gro and. itp files from this to use with GROMACS. So I tried to use the program topolbuild version 1.2 from the GROMACS website. when I execute the command:

[gmx-users] Creating topology for a small organic molecule

Hi. I need to create a topology file for a small organic molecule that is to interact non- covalently with a DNA duplex. I want to use the amber99 force field. I saw on this mailing list that you can use acpypi with antichamber to create a topology for amber force fields. I got the amber10 tools

Re: [gmx-users] Problems with DNA simulation

There were no groups specified in the neutralize.mdp file. I specified the solvent and DNA and it worked. Thanks. On Sun, Sep 20, 2009 at 2:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Gunnar Widtfeldt Reginsson wrote: Hi. I am new to Gromacs and I am following the tutorial on http

Re: [gmx-users] Problem with grompp , ffamber99 and ions

22.98977 #endif int the ions.itp And there were no errors Thanks again. On Sun, Sep 20, 2009 at 11:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: Gunnar Widtfeldt Reginsson wrote: Hi. I am trying to run this command on a solvated DNA grompp -f mini_sol.mdp -p topol.top -c DNAneutral.pdb -n

[gmx-users] Problems with DNA simulation

Hi. I am new to Gromacs and I am following the tutorial on http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top I have managed to get the DNA into a water box. When I run genbox I use the ffamber_tip4p.gro water model. When I then run: grompp -f neutralize.mdp -c solved.pdb -p topol

[gmx-users] Problem with grompp , ffamber99 and ions

Hi.I am trying to run this command on a solvated DNA grompp -f mini_sol.mdp -p topol.top -c DNAneutral.pdb -n DNAneutral.ndx and I get this fatal error: --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No

[gmx-users] Another problem with DNA

I am trying to run grompp using a pdb file of DNA duplex, a sucessfully generated topology, and the steep.mpd from http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top I am getting the fatal error: Fatal error: [ file spc.itp, line 37 ]: Atom index (1) in bonds out of bounds (1-0).

Re: [gmx-users] pdb2gmx with amber99 can't find an atom in a DNA duplex

Problem is solved. The atom needed to be called O not O2. Thanks, On Tue, Sep 15, 2009 at 11:29 PM, Justin A. Lemkul jalem...@vt.edu wrote: Gunnar Widtfeldt Reginsson wrote: Hi. Can someone please help me. I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on. I start

[gmx-users] Re: Another problem with DNA

I tried to modify the spc.itp file, but wasn't successful. I decided not to try any more and changed to the amber_tip4p water model in the .top file. That solved the problem, no more error messages. Thanks for your help. On Wed, Sep 16, 2009 at 7:30 PM, Gunnar Widtfeldt Reginsson regins

[gmx-users] pdb2gmx with amber99 can't find an atom in a DNA duplex

Hi. Can someone please help me. I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on. I start by making a topology file form the pdb file. When I run pdb2gmx and the amber99 force field I get this fatal error:'Atom 02 in residue DT 3 not found in rtp entry with 32 atoms while