Re: [gmx-users] DNA not wrapping around CNT in MD simulation
Okay, thanks, I'll try longer simulations. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Fri, April 22, 2011 5:18:50 PM Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation majid hasan wrote: Okay, thanks, I removed restraints from water. In the final simulation, I increased the simulation time from 20ps to 2000ps to see if they wrap around. However in .trr output, CNT and DNA remain stable, jiggles around and jump across the box in a weird manner (might have something to do with periodic boundary conditions?) but don't seem to be attracted towards each other. 2 ns is still what would be considered an extremely short simulation. Large-scale behavior may take tens or hundreds of ns. I have no experience with DNA-CNT interactions, but for protein-protein interactions (even for small peptides), such time scales are certainly necessary. Movie of output is here: http://phas.ubc.ca/~majid/Project/msteps/cntdna2000ps.mpg I don't see anything odd about this at all. If you're having periodicity issues, trjconv is the tool to take care of that. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow and input em.mdp, and md.mdp files are here: EM: http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdpMD: http://phas.ubc.ca/~majid/Project/msteps/md.mdp Commands that I have been using to build input coordinates, and topologies are below: For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select (Selected amber99sb, and TIP3P water model) For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc (selected amber99sb) For mixing :genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try 20 For solvation: genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro http://phas.ubc.ca/~majid/Project/msteps/md.mdpI have no clue what is wrong with the simulation, and any help is much appreciated. Likely nothing is wrong, you just aren't simulating long enough. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Fri, April 22, 2011 10:59:22 AM *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation majid hasan wrote: Yes, ideally I didn't want to, but I read somewhere on mailing list that one shouldn't use define = -DFLEXIBLE while running dynamics. So I thought I will use restrained water... I'll move back to -DFLEXIBLE though, if I got a successful mdrun for restrained water. Constraints and restraints are separate ideas. http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints If you *restrain* the water, the molecules won't move. If you *constrain* (i.e., using rigid water and not -DFLEXIBLE, which for MD you shouldn't be doing) you fix the geometry of a molecule while still allowing it to actually move. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Fri, April 22, 2011 10:44:45 AM *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation majid hasan wrote: I just checked and DNA position should not be restrained because I didn't use define = -DPOSRES in .mdp file. I am going to run it for a longer time now, and use position restraints for water What purpose does restraining the water have? You'll be trying to observe diffusion of your DNA or CNT through an immobile solvent. -Justin Thank You, Majid. *From:* Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Fri, April 22, 2011 1:51:47 AM *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation On 4/22/2011 6:48 PM, Mark Abraham wrote: On 4/22/2011 4:54 PM, majid hasan wrote: Dear All, I am doing a MD simulation of dna, and cnt in water. I get a stable simulation in which DNA, and CNT wiggles around there positions, but they don't seem to be attracted towards each other. CNT starts in the middle of the box and just moves a little, and DNA starts at top right corner of the box and remains there throughout the simulation. movie of .trr file is here: http
[gmx-users] DNA not wrapping around CNT in MD simulation
Dear All, I am doing a MD simulation of dna, and cnt in water. I get a stable simulation in which DNA, and CNT wiggles around there positions, but they don't seem to be attracted towards each other. CNT starts in the middle of the box and just moves a little, and DNA starts at top right corner of the box and remains there throughout the simulation. movie of .trr file is here: http://phas.ubc.ca/~majid/Project/cntdna.mpg My .mdp files are placed here (both .mdp files are same except for the value of integrator): http://phas.ubc.ca/~majid/Project/lbfgs.mdp (used for EM) http://phas.ubc.ca/~majid/Project/md.mdp (used for MD) I created cnt, and dna using following commands: For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select (Selected amber99sb, and TIP3P water model) For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc (selected amber99sb) For mixing and solvation: genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try 20 genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro In the dna.top file, amber99sb/ions.itp, and a position restraint file was also included along with tip3p.itp. I mentioned it because I am not sure why would it add ions and position restraints on adding water? It seems that something is wrong with non-bonded interactions, but I don't understand what? Thanks for your help, Majid-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DNA not wrapping around CNT in MD simulation
I just checked and DNA position should not be restrained because I didn't use define = -DPOSRES in .mdp file. I am going to run it for a longer time now, and use position restraints for water Thank You, Majid. From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, April 22, 2011 1:51:47 AM Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation On 4/22/2011 6:48 PM, Mark Abraham wrote: On 4/22/2011 4:54 PM, majid hasan wrote: Dear All, I am doing a MD simulation of dna, and cnt in water. I get a stable simulation in which DNA, and CNT wiggles around there positions, but they don't seem to be attracted towards each other. CNT starts in the middle of the box and just moves a little, and DNA starts at top right corner of the box and remains there throughout the simulation. movie of .trr file is here: http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg My .mdp files are placed here (both .mdp files are same except for the value of integrator): http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp (used for EM) http://phas.ubc.ca/%7Emajid/Project/md.mdp (used for MD) I created cnt, and dna using following commands: For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select (Selected amber99sb, and TIP3P water model) For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc (selected amber99sb) For mixing and solvation: genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try 20 genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro In the dna.top file, amber99sb/ions.itp, and a position restraint file was also included along with tip3p.itp. I mentioned it because I am not sure why would it add ions and position restraints on adding water? #including molecule .itp files adds nothing to the system - only the potential to have molecule type(s). The system is defined in the [system] directive, and must match the corresponding coordinate file. It seems that something is wrong with non-bonded interactions, but I don't understand what? Why aren't you following a proper equilibration protocol before trying to make observations? You might be using position restraints, have your species too far apart, or simply have not simulated long enough to observe any movement. 200ps is an eye-blink. Actually, you simulated 20ps. Your MD timestep is 0.2fs, which is unreasonably short. 100,000 of them is far too short to see anything happen. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DNA not wrapping around CNT in MD simulation
Yes, ideally I didn't want to, but I read somewhere on mailing list that one shouldn't use define = -DFLEXIBLE while running dynamics. So I thought I will use restrained water... I'll move back to -DFLEXIBLE though, if I got a successful mdrun for restrained water. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, April 22, 2011 10:44:45 AM Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation majid hasan wrote: I just checked and DNA position should not be restrained because I didn't use define = -DPOSRES in .mdp file. I am going to run it for a longer time now, and use position restraints for water What purpose does restraining the water have? You'll be trying to observe diffusion of your DNA or CNT through an immobile solvent. -Justin Thank You, Majid. *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Fri, April 22, 2011 1:51:47 AM *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation On 4/22/2011 6:48 PM, Mark Abraham wrote: On 4/22/2011 4:54 PM, majid hasan wrote: Dear All, I am doing a MD simulation of dna, and cnt in water. I get a stable simulation in which DNA, and CNT wiggles around there positions, but they don't seem to be attracted towards each other. CNT starts in the middle of the box and just moves a little, and DNA starts at top right corner of the box and remains there throughout the simulation. movie of .trr file is here: http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg My .mdp files are placed here (both .mdp files are same except for the value of integrator): http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp (used for EM) http://phas.ubc.ca/%7Emajid/Project/md.mdp (used for MD) I created cnt, and dna using following commands: For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select (Selected amber99sb, and TIP3P water model) For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc (selected amber99sb) For mixing and solvation: genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try 20 genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro In the dna.top file, amber99sb/ions.itp, and a position restraint file was also included along with tip3p.itp. I mentioned it because I am not sure why would it add ions and position restraints on adding water? #including molecule .itp files adds nothing to the system - only the potential to have molecule type(s). The system is defined in the [system] directive, and must match the corresponding coordinate file. It seems that something is wrong with non-bonded interactions, but I don't understand what? Why aren't you following a proper equilibration protocol before trying to make observations? You might be using position restraints, have your species too far apart, or simply have not simulated long enough to observe any movement. 200ps is an eye-blink. Actually, you simulated 20ps. Your MD timestep is 0.2fs, which is unreasonably short. 100,000 of them is far too short to see anything happen. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DNA not wrapping around CNT in MD simulation
Okay, thanks, I removed restraints from water. In the final simulation, I increased the simulation time from 20ps to 2000ps to see if they wrap around. However in .trr output, CNT and DNA remain stable, jiggles around and jump across the box in a weird manner (might have something to do with periodic boundary conditions?) but don't seem to be attracted towards each other. Movie of output is here: http://phas.ubc.ca/~majid/Project/msteps/cntdna2000ps.mpg and input em.mdp, and md.mdp files are here: EM: http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp MD: http://phas.ubc.ca/~majid/Project/msteps/md.mdp Commands that I have been using to build input coordinates, and topologies are below: For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select (Selected amber99sb, and TIP3P water model) For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc (selected amber99sb) For mixing :genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try 20 For solvation: genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro I have no clue what is wrong with the simulation, and any help is much appreciated. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Fri, April 22, 2011 10:59:22 AM Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation majid hasan wrote: Yes, ideally I didn't want to, but I read somewhere on mailing list that one shouldn't use define = -DFLEXIBLE while running dynamics. So I thought I will use restrained water... I'll move back to -DFLEXIBLE though, if I got a successful mdrun for restrained water. Constraints and restraints are separate ideas. http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints If you *restrain* the water, the molecules won't move. If you *constrain* (i.e., using rigid water and not -DFLEXIBLE, which for MD you shouldn't be doing) you fix the geometry of a molecule while still allowing it to actually move. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Fri, April 22, 2011 10:44:45 AM *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation majid hasan wrote: I just checked and DNA position should not be restrained because I didn't use define = -DPOSRES in .mdp file. I am going to run it for a longer time now, and use position restraints for water What purpose does restraining the water have? You'll be trying to observe diffusion of your DNA or CNT through an immobile solvent. -Justin Thank You, Majid. *From:* Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Fri, April 22, 2011 1:51:47 AM *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation On 4/22/2011 6:48 PM, Mark Abraham wrote: On 4/22/2011 4:54 PM, majid hasan wrote: Dear All, I am doing a MD simulation of dna, and cnt in water. I get a stable simulation in which DNA, and CNT wiggles around there positions, but they don't seem to be attracted towards each other. CNT starts in the middle of the box and just moves a little, and DNA starts at top right corner of the box and remains there throughout the simulation. movie of .trr file is here: http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg My .mdp files are placed here (both .mdp files are same except for the value of integrator): http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp (used for EM) http://phas.ubc.ca/%7Emajid/Project/md.mdp(used for MD) I created cnt, and dna using following commands: For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select (Selected amber99sb, and TIP3P water model) For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc (selected amber99sb) For mixing and solvation: genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try 20 genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro In the dna.top file, amber99sb/ions.itp, and a position restraint file was also included along with tip3p.itp. I mentioned it because I am not sure why would it add ions and position restraints on adding water? #including molecule .itp files adds nothing to the system - only the potential to have molecule type(s). The system is defined in the [system] directive, and must match the corresponding coordinate file. It seems that something is wrong with non-bonded interactions, but I don't understand what? Why aren't you following a proper equilibration protocol before trying to make observations? You might be using position restraints, have
Re: [gmx-users] dna and cnt get distorted in md simulation
first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Thank You, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, April 21, 2011 4:02:57 AM Subject: Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added nsttcouple = -1 value, changed valued of comm_mode from Angular to Linear, changed ns_type value from grid to simple, changed rcoulomb and rvdw values from 0.9 to 1, Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) Is this the file that has had the above modifications made to it for MD? If so, please post the actual file, not the unmodified one. http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file) It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. Why are you employing the free energy code? It seems to me this could be the source of your problems. Each molecule alone is fine, but then by decoupling van der Waals and Coulombic interactions between them, you could be getting instability. Turn off the free energy options and see if you get stable trajectories. -Justin Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dna and cnt get distorted in md simulation
Okay, so here is the file that I used for both energy minimization (with integrator = l-bfgs), and MD (integrator = md). Everything other than the value of integrator was same for both energy minimization and MD. http://phas.ubc.ca/~majid/md.mdp and here is what I see by running .trr files obtained from EM, and MD. On running EM.trr file: In the beginning of simulation, DNA is very stretched i.e atoms of DNA are widely separated from each other, and CNT crumples. Then, gradually DNA shrinks and converges onto CNT. On running MD.trr file: CNT suddenly moves toward and DNA and one part is mixed with DNA and whole structure is crumpled (similar to the final state of EM.trr simulation). Then this crumpled structure wiggles around until the end of simulation. Yes, I ran the whole process in vacuum. I am going to do this simulation by changing cutoff to shift, and see which one works better, and then I will do it with a solvent. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Thu, April 21, 2011 10:25:35 AM Subject: Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. The reason I asked is that the two are very different - one is for MD and the other is for EM, and in some cases, many of the options are irrelevant for either process so it is somewhat hard to deduce what you're actually trying to accomplish with each, especially given the differences. It is best to only post the actual .mdp files you're using and a description of the output corresponding to each. In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. So, the first .mdp file is the one that actually specifies an MD run, not EM? Or does first correspond to the order of the workflow? It might be best to focus on one process at a time, rather than trying to troubleshoot both EM and MD with some arbitrary designators. CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Bonds don't break or form during classical MD. Any bonds forming or breaking are simply a visualization artifact since you're not reading a topology into the visualization software. From your description, it sounds like these simulations are being conducted in vacuo? I tend to suspect that is the source of the problems. Plain cutoffs for electrostatics lead to nasty artifacts and the presence of a highly charged molecule (DNA) that has no shielding between these charges is quite likely to become very distorted due to its own intrinsic repulsion. -Justin Thank You, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thu, April 21, 2011 4:02:57 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added nsttcouple = -1 value, changed valued of comm_mode from Angular to Linear, changed ns_type value from grid to simple, changed rcoulomb and rvdw values from 0.9 to 1, Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) Is this the file that has had the above modifications made to it for MD? If so, please post the actual file, not the unmodified one. http://phas.ubc.ca/~majid
Re: [gmx-users] dna and cnt get distorted in md simulation
Okay, thank you very much. Sounds very plausibly, I will look up the .itp files for bonded interactions of CNT. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Thu, April 21, 2011 12:01:46 PM Subject: Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: Okay, so here is the file that I used for both energy minimization (with integrator = l-bfgs), and MD (integrator = md). Everything other than the value of integrator was same for both energy minimization and MD. http://phas.ubc.ca/~majid/md.mdp and here is what I see by running .trr files obtained from EM, and MD. On running EM.trr file: In the beginning of simulation, DNA is very stretched i.e atoms of DNA are widely separated from each other, and CNT crumples. Then, gradually DNA shrinks and converges onto CNT. OK, so the DNA is experiencing the charge repulsion I described earlier. The CNT sounds like it does not have proper bonded interactions assigned. On running MD.trr file: CNT suddenly moves toward and DNA and one part is mixed with DNA and whole structure is crumpled (similar to the final state of EM.trr simulation). Then this crumpled structure wiggles around until the end of simulation. If EM is showing such weird results, then you can't really trust anything you see in the MD afterwards. Yes, I ran the whole process in vacuum. I am going to do this simulation by changing cutoff to shift, and see which one works better, and then I will do it with a solvent. There is no point in making this assessment in vacuo and then transferring it to solution. Plain cutoffs should not be used. Their artifacts are well-known and modern simulations should not use them. Shifted functions have discontinuities at their longest cutoff and neglect electrostatic interactions beyond this cutoff. Your best option in solution (especially for highly-charged molecules like DNA) is PME. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Thu, April 21, 2011 10:25:35 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: first .mdp file is the original one, and modified .mdp is the one where I made modifications, and I have tried both, and both lead to stable structures for individual molecules, and distorted structures for combined system. The reason I asked is that the two are very different - one is for MD and the other is for EM, and in some cases, many of the options are irrelevant for either process so it is somewhat hard to deduce what you're actually trying to accomplish with each, especially given the differences. It is best to only post the actual .mdp files you're using and a description of the output corresponding to each. In the first .mdp file, free energy calculations are turned off, but even with this file, I get huge distortions in the shape of molecules. So, the first .mdp file is the one that actually specifies an MD run, not EM? Or does first correspond to the order of the workflow? It might be best to focus on one process at a time, rather than trying to troubleshoot both EM and MD with some arbitrary designators. CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. Bonds don't break or form during classical MD. Any bonds forming or breaking are simply a visualization artifact since you're not reading a topology into the visualization software. From your description, it sounds like these simulations are being conducted in vacuo? I tend to suspect that is the source of the problems. Plain cutoffs for electrostatics lead to nasty artifacts and the presence of a highly charged molecule (DNA) that has no shielding between these charges is quite likely to become very distorted due to its own intrinsic repulsion. -Justin Thank You, Majid *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thu, April 21, 2011 4:02:57 AM *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation majid hasan wrote: Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran
[gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt
Dear All, I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide me what can be the possible issues here, and how can I improve it? Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for md simulations. Thank You, Majid-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt
Okay, thanks. But then does it make any big difference on mdrun if we don't minimize energy first? And one more thing, any idea how long it may take to run md for 367 atoms on a laptop with 2GB ram, and dual core 1.4GHz processor. I am just wondering if it is possible to get any results from mdrun on laptop? Thanks again, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, April 20, 2011 11:47:09 AM Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan wrote: Dear All, I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide me what can be the possible issues here, and how can I improve it? Energy minimization and dynamics are independent processes. You should not expect large structural changes during EM with any of the methods. Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for md simulations. Always start with the primary literature: dx.doi.org/10.1002/prot.22711 -Justin Thank You, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt
Okay, thanks a lot. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Wed, April 20, 2011 12:01:33 PM Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan wrote: Okay, thanks. But then does it make any big difference on mdrun if we don't minimize energy first? You should always run energy minimization. What I'm saying is that you should not expect to see any major changes or important phenomena evolve when simply running EM. And one more thing, any idea how long it may take to run md for 367 atoms on a laptop with 2GB ram, and dual core 1.4GHz processor. I am just wondering if it is possible to get any results from mdrun on laptop? You can get results, but that depends entirely upon how much of the processor is being used to do other things at the same time. For a small system, running locally may be an option, but for anything larger than a few hundred atoms you're better off running on a real cluster to avoid performance loss. It will certainly work, but probably not as fast as you might need for very long simulations. -Justin Thanks again, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 20, 2011 11:47:09 AM *Subject:* Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan wrote: Dear All, I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide me what can be the possible issues here, and how can I improve it? Energy minimization and dynamics are independent processes. You should not expect large structural changes during EM with any of the methods. Moreover, what is the right value of nstlist for amber99sb-ildn forcefield for md simulations. Always start with the primary literature: dx.doi.org/10.1002/prot.22711 -Justin Thank You, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] dna and cnt get distorted in md simulation
Dear All, I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then ran the mdrun with integrator = md. I am using a small ssDNA consisting of two residues only (66 atoms), and a small CNT of about 80 atoms. My commands are: For energy minimization, grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 20 mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd and then I ran molecular dyamics, grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20 mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd For individual DNA, and CNT alone, both produce reasonable results, where molecule stays together and jiggles around. However on combining the two molecules, both energy minimization and mdrun lead to distorted structures: bond lengths don't remain fixed neither for CNT nor for DNA, and atoms of both molecules get intertwined and produce a mess. I tried two .mdp files. I got the first .mdp from a colleague who used it for a simple simulation of CNT only (without solvent, and any other molecule) . I made few changes in this file after going through manual e.g enabled free energy calculations, added nsttcouple = -1 value, changed valued of comm_mode from Angular to Linear, changed ns_type value from grid to simple, changed rcoulomb and rvdw values from 0.9 to 1, Both .mdp files are placed at following addresses: http://phas.ubc.ca/~majid/md.mdp (first .mdp file) http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file) It seems to me that problem might be related to non-bonded interaction because this is the significant difference between one and two molecule system. Any help would be much appreciated. Thanks, Majid-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] atomname2type.n2t file for CNT in amber99
Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUB CA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C 0 12.011 3C 0.142 C 0.142 C 0.142 CA CA0 12.011 2C 0.142 C 0.142 CA CB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C 12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. Any help is much appreciated. Thanks, Majid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] atomname2type.n2t file for CNT in amber99
Yes, I saved this atomname2type.n2t file in amber99.ff, and my g_x2top command was: g_x2top -f cnt.gro -o cnt.top -ff select, and then I selected amber99 (4th option). Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, April 19, 2011 10:40:53 AM Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUB CA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C 0 12.011 3C 0.142 C 0.142 C 0.142 CA CA0 12.011 2C 0.142 C 0.142 CA CB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C 12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] atomname2type.n2t file for CNT in amber99
Just a little addition to my previous reply: if I run the same procedure with oplsaa, it works. Now in Oplsaa, I added following two lines in already existing .n2t lines, CAopls_239 0 12.011 3C 0.142 C 0.142 C 0.142 CAopls_239 0 12.011 2C 0.142 C 0.142 But oplsaa also has a bunch of other atoms named opls... , but I guess these don't matter because nanotube only has Carbon bonded with 1,2, or 3, atoms, so I only added three lines for these carbons in amber99.n2t Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, April 19, 2011 10:40:53 AM Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUB CA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C 0 12.011 3C 0.142 C 0.142 C 0.142 CA CA0 12.011 2C 0.142 C 0.142 CA CB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C 12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] atomname2type.n2t file for CNT in amber99
Actually, I just restarted my computer, and now it worked. When I create the topology file using the same procedure, I get a cnt.top file with atoms C, and CB, which correspond to carbons with two and three bonds. Thanks for your help, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Tue, April 19, 2011 11:47:44 AM Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Just a little addition to my previous reply: if I run the same procedure with oplsaa, it works. Now in Oplsaa, I added following two lines in already existing .n2t lines, CAopls_2390 12.011 3C 0.142 C 0.142 C 0.142 CAopls_239 0 12.011 2C 0.142 C 0.142 But oplsaa also has a bunch of other atoms named opls... , but I guess these don't matter because nanotube only has Carbon bonded with 1,2, or 3, atoms, so I only added three lines for these carbons in amber99.n2t You don't need to account for every possible atom, just what your system deals with. Ideally, the .n2t file would be setup such that any molecule would have its topology properly generated, but that is a rather complex (and perhaps unattainable) task. If you send me your coordinate file and Amber99 .n2t file (off-list) I will try to debug what's going on. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, April 19, 2011 10:40:53 AM *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUBCA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C0 12.011 3C 0.142 C 0.142 C 0.142 CACA0 12.011 2C 0.142 C 0.142 CACB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] atomname2type.n2t file for CNT in amber99
Yea, sure, thanks. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Tue, April 19, 2011 12:09:06 PM Subject: Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Actually, I just restarted my computer, and now it worked. When I create the topology file using the same procedure, I get a cnt.top file with atoms C, and CB, which correspond to carbons with two and three bonds. Then it sounds like something in your shell environment is not set properly, either sourcing the wrong GMXRC or setting PATHs or something similar incorrectly. Keep this in mind for the future. -Justin Thanks for your help, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Tue, April 19, 2011 11:47:44 AM *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Just a little addition to my previous reply: if I run the same procedure with oplsaa, it works. Now in Oplsaa, I added following two lines in already existing .n2t lines, CAopls_2390 12.011 3C 0.142 C 0.142 C 0.142 CAopls_239 0 12.011 2C 0.142 C 0.142 But oplsaa also has a bunch of other atoms named opls... , but I guess these don't matter because nanotube only has Carbon bonded with 1,2, or 3, atoms, so I only added three lines for these carbons in amber99.n2t You don't need to account for every possible atom, just what your system deals with. Ideally, the .n2t file would be setup such that any molecule would have its topology properly generated, but that is a rather complex (and perhaps unattainable) task. If you send me your coordinate file and Amber99 .n2t file (off-list) I will try to debug what's going on. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Tue, April 19, 2011 10:40:53 AM *Subject:* Re: [gmx-users] atomname2type.n2t file for CNT in amber99 majid hasan wrote: Dear All, In an attempt to create CNT topology with g_x2top and amber99, I was getting this error: no or incorrect atomname2type.n2t file found. So I tried to create a atomname2type.n2t file for CNT in Amber99. My coordinate file is of this form: UNNAMED 400 1TUBCA1 0.392 0.000 0.000 so I opened oplsaa's .n2t file, and replaced all the entries with these three lines: CA C0 12.011 3C 0.142 C 0.142 C 0.142 CACA0 12.011 2C 0.142 C 0.142 CACB0 12.011 1C 0.142 C, CA, CB are all listed in atomtypes.atp file in Amber as: C12.01000; sp2 C carbonyl group CA12.01000; sp2 C pure aromatic (benzene) CB12.01000; sp2 aromatic C, 56 membered ring junction But when I run the g_x2top, I still get the same error. And where is this .n2t file located? It needs to be in the amber99.ff directory to actually work, and you need to provide this force field's name in your g_x2top command, which unfortunately you have not posted. -Justin Any help is much appreciated. Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users
[gmx-users] Simulation of CNT with Amber forcefield
Dear All, I am doing a DNA-CNT simulation, and I am trying to generate a topology of CNT using Amber99, which has been used for such systems, and CNT atoms are modeled using sp2 carbon parameters. But when I try to create topology file using: pdb2gmx -f cnt.pdb -p cnt.top, and Amber99 forcefield, I get this error: Fatal Error: Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms while sorting atoms. During the execution, it says There are 1 chains and 0 blocks of water and 1 residues with 168 atoms after analyzing pdb file. So I suspect problem is that it reads carbon as a residue in my .pdb file. If this is the problem, then how do I make sure that it reads carbon as an atom and not a residue? My .pdb file has entries of the form: ATOM 1 C C A 1 4.039 ATOM 2 C C A 1 3.97 Thanks for your help, Majid-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of CNT with Amber forcefield
Okay, so I am able to create cnt.rtp, and cnt.top file using g_x2top. But g_x2top only supports OPLSAA, and GROMOS forcefield, and if I use a different forcefield then I get this error: Fatal Error: No or incorrect atomname2type.n2t file found, which is because other forcefields don't contain any .n2t files. And, I don't want to create cnt.top using oplsaa/gromos because these forcefields are not suitable for dna. So what is the way around i.e if I can't use the same force field to construct both (cnt and dna) topologies, then what do I do? Is any of following likely to work (though I don't think so): 1) Create cnt.top and cnt.rtp using x2top oplsaa, and add cnt.rtp in amber? 2) Add an atomname2type.n2t in amber? Lastly, the link http://cs86.com/CNSE/SWNT.htm doesn't contain anything at the moment. Has it been replaced by some other link or is it permanently down? Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, April 18, 2011 10:25:39 AM Subject: Re: [gmx-users] Simulation of CNT with Amber forcefield majid hasan wrote: Dear All, I am doing a DNA-CNT simulation, and I am trying to generate a topology of CNT using Amber99, which has been used for such systems, and CNT atoms are modeled using sp2 carbon parameters. But when I try to create topology file using: pdb2gmx -f cnt.pdb -p cnt.top, and Amber99 forcefield, I get this error: Have you created an .rtp entry for your CNT? I doubt that it's even possible for cyclic molecules like this one. pdb2gmx is only useful for linear molecules composed of repeating building blocks, with limited support for branching. You may want to consult: http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube Some of that information is outdated, but there is a plethora of information in the list archive about proper CNT topology generation. Search for posts by Christopher Stiles. Fatal Error: Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms while sorting atoms. This answers my question above. Your structure is being interpreted as RNA. Without significant effort and perhaps code modification, pdb2gmx is not likely to be useful here. During the execution, it says There are 1 chains and 0 blocks of water and 1 residues with 168 atoms after analyzing pdb file. So I suspect problem is that it reads carbon as a residue in my .pdb file. If this is the problem, then how do I make sure that it reads carbon as an atom and not a residue? My .pdb file has entries of the form: ATOM 1 C C A 1 4.039 ATOM 2 C C A 1 3.97 Well, you've named your residues C and the component atoms C so there's no real confusion about anything. It's also not the source of your problems. g_x2top may be a useful program for generating a topology, or perhaps other software that is entirely unrelated to Gromacs. -Justin Thanks for your help, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genbox output taking forever to complete
Okay, so here is an output attached, for cubic box of length 10 (I removed some atoms to reduce the size below 50kB). Actually, the carbon atoms are all placed at 0x4, 0 y 2.5,0z3.5. While solvent and DNA atoms are in the region 4x,y,z6. So only DNA is solvated, while CNT is just lying outside. Though I might have placed solvent in a cube of length 10 (using: editconf -f spc216.pdb -o spc216.gro -box 10 10 10), could this be the reason? I am at the moment trying to solvate the whole system (in a cubic box of 20) without specifying -box in editconf -o spc216.gro, but this is taking long, its running for about half an hour after reaching this point: Reading solvent configuration Quotation Solvent configuration contains 648 atoms in 216 residues. Is that much time normal, I am running it on my laptop, which is 2GB Ram, and Dual Core ~1.4GHz processor? Thanks a lot, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 17, 2011 4:39:56 AM Subject: Re: [gmx-users] genbox output taking forever to complete majid hasan wrote: Okay, so I divided the procedure in three steps, and this does produce output immediately. But it seems that it doesn't put second molecule inside the box. Here is the what I am doing: 1. editconf -f ssgcg.pdb -o ssgcg.gro -box 20 20 20 2. genbox -cp ssgcg.gro -ci cntcapped.pdb -nmol 1 -o cntdna.gro 3. editconf -f spc216.pdb -o spc216.gro -box 20 20 20 4. genbox -cp cntdna.gro -cs spc216.gro -o solvated.gro 5. editconf -f solvated.gro -o solvated.pdb I tried cubic boxes of different lenghts (10, 20, 100), but when I see the final file in solvated.pdb in rasmol, it seems that it puts dna, and cnt at a distance equal to the specified length of the box, and the water molecules are all clustered around dna only. I also tried to create a box of lenght 100 20 20 and align dna along 1 0 0, but I still got the similar final output. My question is, what determines the distance between molecules inside the box, and how can I make sure that they are placed at a reasonable distance inside the solvent? I'm not entirely clear on what you're seeing, but you need to omit step 3 above. Defining a huge box for a small cube of solvent will lead to incorrect solvation. genbox will read a solvent configuration and create identical blocks until the unit cell is full. Defining a larger box in which you place the solvent prevents this from working. Positions of molecules inserted with genbox -ci -nmol are random. If you want to define a specific orientation or position in the box, use editconf -center/-translate/-rotate as necessary. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Sat, April 16, 2011 6:19:39 PM *Subject:* Re: [gmx-users] genbox output taking forever to complete Justin A. Lemkul wrote: majid hasan wrote: Dear All, I am trying to add a single strand dna, and single walled carbon nanotube in a box using the genbox command. After typing following command: genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro, I get: Reading solute configuration Containing 168 atoms in 1 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration Giving Russians Opium May Alter Current Situation solvent configuration contains 648 atoms in 216 residues and then it takes forever to produce output. I tried to generate an output with just one molecule in solvent (spc216.gro), and I ran into same problem. I suspect something is wrong with my solvent input (file attached). I copied this file from gromacs/tutor/water folder, though it looks reasonable when I view I view the corresponding .pdb file in rasmol (I created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). Could anyone please guide me about possible issues, and how to resolve them? You're asking genbox to do far too many things at once. Divide your procedure into steps: 1. Set a box size using editconf for either the CNT or DNA. I should say a sensible box size - a 2x2x2 box barely accommodates the smallest DNA fragment, and then certainly does not leave any room at all to accommodate the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department
Re: [gmx-users] genbox output taking forever to complete
Okay, thank you. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 17, 2011 12:28:47 PM Subject: Re: [gmx-users] genbox output taking forever to complete majid hasan wrote: Okay, so here is an output attached, for cubic box of length 10. Actually, the carbon atoms are all placed at 0x4, 0 y 2.5, 0z3.5. While solvent and DNA atoms are in the region 4x,y,z6. So Then your box size is overkill. All you're going to end up doing is adding tens of thousands of waters that do not serve any purpose for most applications. There is (in general) no need for a 4-nm buffer around your system. Take your unsolvated coordinate file and run editconf -d 1 to obtain a more suitable box before trying genbox again. only DNA is solvated, while CNT is just lying outside. Though I might have placed solvent in a cube of length 10 (using: editconf -f spc216.pdb -o spc216.gro -box 10 10 10), could this be the reason? Yes, as I said before - do not adjust the box of spc216.gro. The genbox program takes the input solvent configuration (unmodified, please!) and tiles it across the box defined in the -cp configuration such that it fills the box. If you make a solvent box with a bunch of empty space just to fit in your existing box, you accomplish nothing at all and genbox will probably chew up a lot of memory trying to make this exact fit. I am at the moment trying to solvate the whole system (in a cubic box of 20) without specifying -box in editconf -o spc216.gro, but this is taking long, its running for about half an hour after reaching this point: Reading solvent configuration Quotation Solvent configuration contains 648 atoms in 216 residues. Is that much time normal, I am running it on my laptop, which is 2GB Ram, and Dual Core ~1.4GHz processor? That is an enormous box that will require a large amount of memory to accomplish. Before trying to get a huge box to work, make sure you can do something more normal as I suggest above. You haven't stated your overall purpose, but for only a very few particular tasks would you ever require a system this large for components as small as the ones you're dealing with. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genbox output taking forever to complete
Alright, thanks. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 17, 2011 12:31:49 PM Subject: Re: [gmx-users] genbox output taking forever to complete majid hasan wrote: Okay, so here is an output attached, for cubic box of length 10 (I removed some atoms to reduce the size below 50kB). Please do not attach coordinate files unless requested. Most people who are uninterested in this thread do not want to waste time downloading large emails that they don't need. It is substantially more efficient to post a link to an image in a freely accessible place, i.e. point #4: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette Also, ad hoc removal of atoms is not helpful to solving your issue. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] .top file for DNA-CNT
Dear All, I want to simulate DNA-CNT interaction, and reproduce the helical wrapping of DNA around CNT in the first step, and later study the effects of temperature, CNT length etc on the favorable geometries of hybrid. I have created .top files for DNA, and CNT separately. To generate the top file of entire system (DNA-CNT), I added CNT in a box with DNA using genbox. But when I try to create .top file using pdb2gmx and Amber forcefield, I get an error that atom C in residue 11 C not found in rtp entry because rtp because .rtp file in Amber only contain dna residues, and if I use some other forcefield like oplsaa then dna residues won't be present. So how do I create the .top file for whole system i.e DNA-CNT? Mailing list suggests that another and probably easier way of doing this is to create .itp file for CNT, and add it to dna.top file using #include file mechanism. So I wanted to ask how can I create .itp file from topology file (because I have the toplogy file for CNT), or do I need to create it manually from scratch? Thank You, Majid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .top file for DNA-CNT
Okay, so I just removed #include forcefield from top, and [system] [molecule] directives from the bottom of my topology file, and saved it as .itp file. Is that fine? And, if I #include water topology in dna.itp file, then I shouldn't include it in system's topology file, and it doesn't make any difference whether I include water in a molecule.itp file or I add it explicitly in system topology, right? Moreover, I created cnt.top using oplsaa forcefield, so in my cnt.itp file carbon atoms' type is opls_240. So when I run the grompp using amber99sb-ildn, it gives me the following error: Fatal Error: Atomtype opls_240 not found, which is probably because amber doesn't recognize opls_240. How should I correct the atom type in my cnt.itp file? If I just add an atomtype opls_240 in /amber99sb-ildn.ff/atomtypes.atp, would it be enough? Manual's section 5.8.3 says that after definition of new atom types, additional non-bonded, and pair parameters can be defined. I earlier added some CNT parameters ([bond types], [angle types], ..) in ffoplsaabon.itp, do I need to make exactly the same changes in amber.ff/ffbonded.itp? Is it generally not possible to create topology of one molecule using one forcefield, and then do MD simulation of entire system using another forcefield (without changing parameters etc.)? Thanks for your help, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sun, April 17, 2011 4:54:11 PM Subject: Re: [gmx-users] .top file for DNA-CNT majid hasan wrote: Dear All, I want to simulate DNA-CNT interaction, and reproduce the helical wrapping of DNA around CNT in the first step, and later study the effects of temperature, CNT length etc on the favorable geometries of hybrid. I have created .top files for DNA, and CNT separately. To generate the top file of entire system (DNA-CNT), I added CNT in a box with DNA using genbox. But when I try to create .top file using pdb2gmx and Amber forcefield, I get an error that atom C in residue 11 C not found in rtp entry because rtp because .rtp file in Amber only contain dna residues, and if I use some other forcefield like oplsaa then dna residues won't be present. So how do I create the .top file for whole system i.e DNA-CNT? Mailing list suggests that another and probably easier way of doing this is to create .itp file for CNT, and add it to dna.top file using #include file mechanism. So I wanted to ask how can I create .itp file from topology file (because I have the toplogy file for CNT), or do I need to create it manually from scratch? The conversion of .top to .itp is simple. A .top is a system topology and contains a description of the entire system. An .itp file describes one type of molecule. To create a .itp from a .top, follow this: http://www.gromacs.org/Documentation/File_Formats/.itp_File Then a simple system topology is just: #include (whatever force field) #include cnt.itp #include dna.itp #include spc.itp (or whatever water) #include ions.itp (if needed) Finish with appropriate [system] and [molecules] directives. -Justin Thank You, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .top file for DNA-CNT
Okay, thanks, I'll stick to Amber then. Thanks again, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 17, 2011 6:35:07 PM Subject: Re: [gmx-users] .top file for DNA-CNT majid hasan wrote: Okay, so I just removed #include forcefield from top, and [system] [molecule] directives from the bottom of my topology file, and saved it as .itp file. Is that fine? Yes. And, if I #include water topology in dna.itp file, then I shouldn't include it in system's topology file, and it doesn't make any difference whether I include water in a molecule.itp file or I add it explicitly in system topology, right? Correct. I often find it much simpler to just #include everything in one .top file rather than having unnecessary nested #includes, but do what makes the most sense for yourself. Moreover, I created cnt.top using oplsaa forcefield, so in my cnt.itp file carbon atoms' type is opls_240. So when I run the grompp using amber99sb-ildn, it gives me the following error: Fatal Error: Atomtype opls_240 not found, which is probably because amber doesn't recognize opls_240. Never mix and match force fields. You must have one self-consistent representation of the system. How should I correct the atom type in my cnt.itp file? If I just add an atomtype opls_240 in /amber99sb-ildn.ff/atomtypes.atp, would it be enough? Manual's section 5.8.3 says that after definition of new atom No. You can't simply append one force field's content to another and hope it works. You may be able to form a syntactically correct force field, but it would be a complete hack job that would not give anything close to a reliable simulation. types, additional non-bonded, and pair parameters can be defined. I earlier added some CNT parameters ([bond types], [angle types], ..) in ffoplsaabon.itp, do I need to make exactly the same changes in amber.ff/ffbonded.itp? Leave these files alone. There is no need to alter them in this case. Is it generally not possible to create topology of one molecule using one forcefield, and then do MD simulation of entire system using another forcefield (without changing parameters etc.)? In general, no, force fields cannot be combined in this way. There are limited exceptions, but this case is not one of them. You need to choose a parent force field that is suitable for all components of your system and derive molecule topologies from this force field. Mixing and matching will be a great way to waste time. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Thanks for your help, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Sun, April 17, 2011 4:54:11 PM *Subject:* Re: [gmx-users] .top file for DNA-CNT majid hasan wrote: Dear All, I want to simulate DNA-CNT interaction, and reproduce the helical wrapping of DNA around CNT in the first step, and later study the effects of temperature, CNT length etc on the favorable geometries of hybrid. I have created .top files for DNA, and CNT separately. To generate the top file of entire system (DNA-CNT), I added CNT in a box with DNA using genbox. But when I try to create .top file using pdb2gmx and Amber forcefield, I get an error that atom C in residue 11 C not found in rtp entry because rtp because .rtp file in Amber only contain dna residues, and if I use some other forcefield like oplsaa then dna residues won't be present. So how do I create the .top file for whole system i.e DNA-CNT? Mailing list suggests that another and probably easier way of doing this is to create .itp file for CNT, and add it to dna.top file using #include file mechanism. So I wanted to ask how can I create .itp file from topology file (because I have the toplogy file for CNT), or do I need to create it manually from scratch? The conversion of .top to .itp is simple. A .top is a system topology and contains a description of the entire system. An .itp file describes one type of molecule. To create a .itp from a .top, follow this: http://www.gromacs.org/Documentation/File_Formats/.itp_File Then a simple system topology is just: #include (whatever force field) #include cnt.itp #include dna.itp #include spc.itp (or whatever water) #include ions.itp (if needed) Finish with appropriate [system] and [molecules] directives. -Justin Thank You, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users
[gmx-users] genbox output taking forever to complete
Dear All, I am trying to add a single strand dna, and single walled carbon nanotube in a box using the genbox command. After typing following command: genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro, I get: Reading solute configuration Containing 168 atoms in 1 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration Giving Russians Opium May Alter Current Situation solvent configuration contains 648 atoms in 216 residues and then it takes forever to produce output. I tried to generate an output with just one molecule in solvent (spc216.gro), and I ran into same problem. I suspect something is wrong with my solvent input (file attached). I copied this file from gromacs/tutor/water folder, though it looks reasonable when I view I view the corresponding .pdb file in rasmol (I created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). Could anyone please guide me about possible issues, and how to resolve them? Thank You, Majid spc216.gro Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genbox output taking forever to complete
Okay, thanks Justin!. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sat, April 16, 2011 6:19:39 PM Subject: Re: [gmx-users] genbox output taking forever to complete Justin A. Lemkul wrote: majid hasan wrote: Dear All, I am trying to add a single strand dna, and single walled carbon nanotube in a box using the genbox command. After typing following command: genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro, I get: Reading solute configuration Containing 168 atoms in 1 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration Giving Russians Opium May Alter Current Situation solvent configuration contains 648 atoms in 216 residues and then it takes forever to produce output. I tried to generate an output with just one molecule in solvent (spc216.gro), and I ran into same problem. I suspect something is wrong with my solvent input (file attached). I copied this file from gromacs/tutor/water folder, though it looks reasonable when I view I view the corresponding .pdb file in rasmol (I created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). Could anyone please guide me about possible issues, and how to resolve them? You're asking genbox to do far too many things at once. Divide your procedure into steps: 1. Set a box size using editconf for either the CNT or DNA. I should say a sensible box size - a 2x2x2 box barely accommodates the smallest DNA fragment, and then certainly does not leave any room at all to accommodate the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genbox output taking forever to complete
Okay, so I divided the procedure in three steps, and this does produce output immediately. But it seems that it doesn't put second molecule inside the box. Here is the what I am doing: 1. editconf -f ssgcg.pdb -o ssgcg.gro -box 20 20 20 2. genbox -cp ssgcg.gro -ci cntcapped.pdb -nmol 1 -o cntdna.gro 3. editconf -f spc216.pdb -o spc216.gro -box 20 20 20 4. genbox -cp cntdna.gro -cs spc216.gro -o solvated.gro 5. editconf -f solvated.gro -o solvated.pdb I tried cubic boxes of different lenghts (10, 20, 100), but when I see the final file in solvated.pdb in rasmol, it seems that it puts dna, and cnt at a distance equal to the specified length of the box, and the water molecules are all clustered around dna only. I also tried to create a box of lenght 100 20 20 and align dna along 1 0 0, but I still got the similar final output. My question is, what determines the distance between molecules inside the box, and how can I make sure that they are placed at a reasonable distance inside the solvent? Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sat, April 16, 2011 6:19:39 PM Subject: Re: [gmx-users] genbox output taking forever to complete Justin A. Lemkul wrote: majid hasan wrote: Dear All, I am trying to add a single strand dna, and single walled carbon nanotube in a box using the genbox command. After typing following command: genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o cntdna.gro, I get: Reading solute configuration Containing 168 atoms in 1 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration Giving Russians Opium May Alter Current Situation solvent configuration contains 648 atoms in 216 residues and then it takes forever to produce output. I tried to generate an output with just one molecule in solvent (spc216.gro), and I ran into same problem. I suspect something is wrong with my solvent input (file attached). I copied this file from gromacs/tutor/water folder, though it looks reasonable when I view I view the corresponding .pdb file in rasmol (I created .gro file from .pdb file using editconf -f spc216.pdb -o spc216.gro). Could anyone please guide me about possible issues, and how to resolve them? You're asking genbox to do far too many things at once. Divide your procedure into steps: 1. Set a box size using editconf for either the CNT or DNA. I should say a sensible box size - a 2x2x2 box barely accommodates the smallest DNA fragment, and then certainly does not leave any room at all to accommodate the minimum image convention. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dangling bond error for dna
Okay, thank you. I'll try to fix it. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 10, 2011 4:17:59 AM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted below. Output of pdb2gmx is attached. You have numerous problems with this .pdb file: 1. All residues are listed as being the 3' end form. Your chain should start with a 5' end, include the middle residues, and end with a 3' form. 2. 5' ends do not have phosphate on them, per force field convention. 3. You have various incorrect atoms, and some incorrect atom names. Please refer to the dna.rtp file for your chosen force field to understand its expectations. Then you will need to manually fix your .pdb file by renaming, replacing, or removing whatever is in conflict. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dangling bond error for dna
Is there any software that generates .pdb file consistent with amber forcefield requirements? I tried 3DNA, and GABEDIT, but 3DNA doesn't name residues in correct format i.e DX, and gabedit names every residue as DX3. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 10, 2011 4:17:59 AM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted below. Output of pdb2gmx is attached. You have numerous problems with this .pdb file: 1. All residues are listed as being the 3' end form. Your chain should start with a 5' end, include the middle residues, and end with a 3' form. 2. 5' ends do not have phosphate on them, per force field convention. 3. You have various incorrect atoms, and some incorrect atom names. Please refer to the dna.rtp file for your chosen force field to understand its expectations. Then you will need to manually fix your .pdb file by renaming, replacing, or removing whatever is in conflict. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dangling bond error for dna
Okay, I am trying AmberTools as well. Thanks Justin! Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, April 10, 2011 10:16:57 AM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Is there any software that generates .pdb file consistent with amber forcefield requirements? I tried 3DNA, and GABEDIT, but 3DNA doesn't name residues in correct format i.e DX, and gabedit names every residue as DX3. Perhaps xleap (part of AmberTools), but if your input has a bunch of incorrect atoms, I don't know how well it deals with replacing them. I seem to remember that it just writes new atoms and doesn't necessarily clean up the old ones, but my memory could be incorrect or the program may have been improved since last I tried it. http://ambermd.org/#AmberTools -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Sun, April 10, 2011 4:17:59 AM *Subject:* Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted below. Output of pdb2gmx is attached. You have numerous problems with this .pdb file: 1. All residues are listed as being the 3' end form. Your chain should start with a 5' end, include the middle residues, and end with a 3' form. 2. 5' ends do not have phosphate on them, per force field convention. 3. You have various incorrect atoms, and some incorrect atom names. Please refer to the dna.rtp file for your chosen force field to understand its expectations. Then you will need to manually fix your .pdb file by renaming, replacing, or removing whatever is in conflict. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Naming of DNA residues, and structure of .pdb file
Okay, thanks a lot. Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sat, April 9, 2011 3:05:48 PM Subject: Re: [gmx-users] Naming of DNA residues, and structure of .pdb file majid hasan wrote: Dear All, I am trying to make sure that the names of dna residues in my .pdb file match with .rtp file in the Amber forcefield. I looked up the residuetypes.dat file (attached), and it gives the names for DNA residues, which are of the form, DX, DX3, DX5, DXN (X=A,C,T,G). So if I have a residue X, then what is the difference between DX, DX3, so on i.e when do I name residue X as DX, and when as DX3, and so on? DX = normal residue DX5 = 5' end DX3 = 3' end Moreover, can anyone explain me the format of pdb file (attached) i.e what do different columns represent, so I can change the names of residues without making any error? http://www.wwpdb.org/documentation/format32/sect9.html -Justin Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Dangling bond error for dna
Dear All, I created .pdb file for dna using gabedit. But when I try to create the topology file I get this error: Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. Output of pdb2gmx, and my input pdb files are attached. Could anyone please suggest why this is happening? Thanks, Majid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dangling bond error for dna
.pdb file size was big, so message didn't deliver. Now I have removed atoms from pdb file to reduce the size, and the files are attached. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sat, April 9, 2011 7:18:30 PM Subject: Re: [gmx-users] Dangling bond error for dna majid hasan wrote: Dear All, I created .pdb file for dna using gabedit. But when I try to create the topology file I get this error: Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. Output of pdb2gmx, and my input pdb files are attached. Could anyone please suggest why this is happening? Nothing is attached. -Justin Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists dna6_atomsremoved.pdb Description: Binary data dangling bond error_output of pdb2gmx Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] .n2t file for ssDNA
Dear All, I am trying to simulate the interaction between DNA, and CNT. But when I try to create the toplogy file with command g_x2top -f ssdna.gro -o ssdna.top -ff select, I get the following error: Fatal error: Could only find a forcefield type for 119 out of 287 atoms I am using the oplsaa forcefield, and I suspect it is because atomname2type.n2t file doesn't contain all the possible bonds in it. Copy of my .n2t file is attached with the message. Could you please guide me how to add all these possible bonds in my .n2t file? I also downloaded the ffoplsaanr, ffoplsaano, from user contributed gromacs forcefields, but these packages also don't have .n2t file. Thanks, Majid atomname2type.n2t Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .n2t file for ssDNA
Thanks Justin! But with pdb2gmx, after selecting force field and water model, I get this error: Fatal Error: Residue 'DA3' not found in residue topology (on selecting oplsaa), and when I selected amber99, I got following fatal error: there is a dangling bond at at least one of the terminal ends and the force field doesn't provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. I also tried Amber, and Oplsaa forcefields on a different dna.pdb file, and got missing residue errors. Any help would be much appreciated. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, April 8, 2011 12:54:38 PM Subject: Re: [gmx-users] .n2t file for ssDNA majid hasan wrote: Dear All, I am trying to simulate the interaction between DNA, and CNT. But when I try to create the toplogy file with command g_x2top -f ssdna.gro -o ssdna.top -ff select, I get the following error: Fatal error: Could only find a forcefield type for 119 out of 287 atoms I am using the oplsaa forcefield, and I suspect it is because atomname2type.n2t file doesn't contain all the possible bonds in it. Copy of my .n2t file is attached with the message. Could you please guide me how to add all these possible bonds in my .n2t file? That would be a very time-consuming exercise, and likely (certainly) g_x2top is not the best tool for this job, for several reasons, the most obvious being that a number of force fields (AMBER and CHARMM, at least) have native support for nucleic acids via pdb2gmx. g_x2top can certainly create a topology for a CNT, but it requires basically one line, since the geometry is all the same. Then just #include your cnt.itp file in your system topology and you're done. -Justin I also downloaded the ffoplsaanr, ffoplsaano, from user contributed gromacs forcefields, but these packages also don't have .n2t file. Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .n2t file for ssDNA
Okay, I'll try to create a better .pdb file, and see how it goes. So if oplsaa doesn't have nucleic acids, then Amber is a better choice? Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Fri, April 8, 2011 3:03:23 PM Subject: Re: [gmx-users] .n2t file for ssDNA majid hasan wrote: Thanks Justin! But with pdb2gmx, after selecting force field and water model, I get this error: Fatal Error: Residue 'DA3' not found in residue topology (on selecting oplsaa), and when I selected amber99, I got following fatal Right, there are no nucleic acids in OPLS-AA by default. There may be parameters out there somewhere, but they're not in Gromacs. error: there is a dangling bond at at least one of the terminal ends and the force field doesn't provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. This is not a broadly-applicable error message, unfortunately, contrary to what it might suggest. Nucleic acid termini do not use .n.tdb or .c.tdb files; these are for proteins. Regardless, your input file has to conform to the requirements of the .rtp entries for the force field. You're probably missing atoms. I also tried Amber, and Oplsaa forcefields on a different dna.pdb file, and got missing residue errors. Then the input is not sound and thus is not a good test case. -Justin Any help would be much appreciated. Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Fri, April 8, 2011 12:54:38 PM *Subject:* Re: [gmx-users] .n2t file for ssDNA majid hasan wrote: Dear All, I am trying to simulate the interaction between DNA, and CNT. But when I try to create the toplogy file with command g_x2top -f ssdna.gro -o ssdna.top -ff select, I get the following error: Fatal error: Could only find a forcefield type for 119 out of 287 atoms I am using the oplsaa forcefield, and I suspect it is because atomname2type.n2t file doesn't contain all the possible bonds in it. Copy of my .n2t file is attached with the message. Could you please guide me how to add all these possible bonds in my .n2t file? That would be a very time-consuming exercise, and likely (certainly) g_x2top is not the best tool for this job, for several reasons, the most obvious being that a number of force fields (AMBER and CHARMM, at least) have native support for nucleic acids via pdb2gmx. g_x2top can certainly create a topology for a CNT, but it requires basically one line, since the geometry is all the same. Then just #include your cnt.itp file in your system topology and you're done. -Justin I also downloaded the ffoplsaanr, ffoplsaano, from user contributed gromacs forcefields, but these packages also don't have .n2t file. Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .n2t file for ssDNA
Yes, of course. But right now I am just trying to make sure that my input files are all correct, and then I will dig into these actual forcefields. Thanks a lot, Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Fri, April 8, 2011 3:14:47 PM Subject: Re: [gmx-users] .n2t file for ssDNA majid hasan wrote: Okay, I'll try to create a better .pdb file, and see how it goes. So if oplsaa doesn't have nucleic acids, then Amber is a better choice? A force field should be chosen based on thorough study of the literature, including the derivation of the parameter sets and their inherent assumptions and limitations, as well as their success in reproducing relevant physical observables. This is the most important choice you likely make when starting a simulation, so you shouldn't simply choose a force field because it's there and might work in terms of getting some form of output. -Justin Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Gromacs Users' List gmx-users@gromacs.org *Sent:* Fri, April 8, 2011 3:03:23 PM *Subject:* Re: [gmx-users] .n2t file for ssDNA majid hasan wrote: Thanks Justin! But with pdb2gmx, after selecting force field and water model, I get this error: Fatal Error: Residue 'DA3' not found in residue topology (on selecting oplsaa), and when I selected amber99, I got following fatal Right, there are no nucleic acids in OPLS-AA by default. There may be parameters out there somewhere, but they're not in Gromacs. error: there is a dangling bond at at least one of the terminal ends and the force field doesn't provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. This is not a broadly-applicable error message, unfortunately, contrary to what it might suggest. Nucleic acid termini do not use .n.tdb or .c.tdb files; these are for proteins. Regardless, your input file has to conform to the requirements of the .rtp entries for the force field. You're probably missing atoms. I also tried Amber, and Oplsaa forcefields on a different dna.pdb file, and got missing residue errors. Then the input is not sound and thus is not a good test case. -Justin Any help would be much appreciated. Thanks, Majid *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Fri, April 8, 2011 12:54:38 PM *Subject:* Re: [gmx-users] .n2t file for ssDNA majid hasan wrote: Dear All, I am trying to simulate the interaction between DNA, and CNT. But when I try to create the toplogy file with command g_x2top -f ssdna.gro -o ssdna.top -ff select, I get the following error: Fatal error: Could only find a forcefield type for 119 out of 287 atoms I am using the oplsaa forcefield, and I suspect it is because atomname2type.n2t file doesn't contain all the possible bonds in it. Copy of my .n2t file is attached with the message. Could you please guide me how to add all these possible bonds in my .n2t file? That would be a very time-consuming exercise, and likely (certainly) g_x2top is not the best tool for this job, for several reasons, the most obvious being that a number of force fields (AMBER and CHARMM, at least) have native support for nucleic acids via pdb2gmx. g_x2top can certainly create a topology for a CNT, but it requires basically one line, since the geometry is all the same. Then just #include your cnt.itp file in your system topology and you're done. -Justin I also downloaded the ffoplsaanr, ffoplsaano, from user contributed gromacs forcefields, but these packages also don't have .n2t file. Thanks, Majid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http
[gmx-users] .pdb file for DNA
Dear All, I want to simulate interaction between single strand dna and cnt. I tried to use Biomer (from case group webpage), but it's not working. When I try to open B.html in my browser, I get a blank page. Could anyone please tell me if there is another way to generate .pbd file for dna? Thanks, Majid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation
So, I installed the development package for x-window-system, and reinstalled both fftw, and gromacs, and now everything seems fine. I do see the animation after running demo. Thanks, Majid From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 9:39:12 PM Subject: Re: [gmx-users] Gromacs Installation On 15/02/2011 4:35 PM, majid hasan wrote: Okay, I'll do this. I have also realized after browsing through config.log, that Xlib.h is absent. Where do I get it, I want it to run ngmx. You will need the X windowing system installed, and probably the associated devel packages. Use your distribution's package manager. Mark Thanks, Majid From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 9:07:15 PM Subject: Re: [gmx-users] Gromacs Installation clean reinstallation. make uninstall make distclean rm -r the untar one from source re-install it again. lina On Tue, Feb 15, 2011 at 12:39 PM, majid hasan pu_majidha...@yahoo.com wrote: Okay. Actually, second time, I over-worte the first installation. I mean I didn't uninstall the first one, I just ran the whole process again starting from fftw$./configure. I am not sure if that is all right, I just did it to find out the problem. In the third attempt (without issuing --enable-shared anywher), I again over-wrote the gromacs installation files, and this went well. It worked, but I don't know why? Best, Majid From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 8:04:38 PM Subject: Re: [gmx-users] Gromacs Installation You are right, it's relevant to the shared libs. but I don't know why you failed in the second attempt if you did a clean reinstallation. lina Food fight? Enjoy some healthy debate in the Yahoo! Answers Food Drink QA. No need to miss a message. Get email on-the-go with Yahoo! Mail for Mobile. Get started. http://mobile.yahoo.com/mail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs Installation
Dear All, I am trying to install gromacs in ubuntu. I configured both fftw and gromacs in my home folder following the instructions on http://www.gromacs.org/Downloads/Installation_Instructions. However, when I do make, I get an error in the end (pasted below). I have also attached the log file of compilation with the email. /usr/bin/ld: /home/majid/user/soft/fftw/lib/libfftw3f.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /home/majid/user/soft/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/majid/user/down/gromacs/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/majid/user/down/gromacs/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/majid/user/down/gromacs/src' make: *** [all-recursive] Error 1 Moreover, I wanted to ask if I can download gromacs in my home directory using the ubuntu software center or synaptic manager? Thanks, Majid Looking for earth-friendly autos? Browse Top Cars by Green Rating at Yahoo! Autos' Green Center. http://autos.yahoo.com/green_center/ log Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation
Okay, I'll try with --enable-single. But as far as I understood, it seems like its an issue with --enable-shared. In the first attempt, I did enable-shared in fftw configuration, but didn't do it in gromacs configuration, and got this error. In the second attempt, I did enable-shared in ./configure for both fftw and gromacs, but still got the same message. In the third attempt, I didn't enable shared anywhere, and installation went well. Only issue is that when I run ngmx, it says command not found, and I can't view .trr file, but this seems to be a different issue. But I don't know why --enable-shared isn't working. About installing in home directory: actually I downloaded the source from gromacs website, and I did manage to install it in my home directory. But some of the commands, like luck, and ngmx are missing. When I type any of luck, I get, command not found and you can install it by typing sudo apt-get install gromacs. I did try to download it using apt-get and software center in ubuntu, but it installs it in usr/share/gromacs, but I want to install it in my home directory. Thanks, Majid From: lina zhao lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 6:24:47 PM Subject: Re: [gmx-users] Gromacs Installation 1. Seems the default fftw configuration is double, when you install the fftw-3.2.2 configure with --enable single. 2. about your question:I wanted to ask if I can download gromacs in my home directory using the ubuntu software center or synaptic manager? 1] You can download in your home directory and install. 2] a better but a bit not so-easy way, is download the source (http://packages.debian.org/sid/gromacs), built the package and add it into repository. There maybe also some other ways. HTH, lina On Tue, Feb 15, 2011 at 6:23 AM, majid hasan pu_majidha...@yahoo.com wrote: Dear All, I am trying to install gromacs in ubuntu. I configured both fftw and gromacs in my home folder following the instructions on http://www.gromacs.org/Downloads/Installation_Instructions. However, when I do make, I get an error in the end (pasted below). I have also attached the log file of compilation with the email. /usr/bin/ld: /home/majid/user/soft/fftw/lib/libfftw3f.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /home/majid/user/soft/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/majid/user/down/gromacs/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/majid/user/down/gromacs/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/majid/user/down/gromacs/src' make: *** [all-recursive] Error 1 Moreover, I wanted to ask if I can download gromacs in my home directory using the ubuntu software center or synaptic manager? Thanks, Majid Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives.Check it out. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Sucker-punch spam with award-winning protection. Try the free Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/features_spam.html-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation
Okay, thanks, I'll look into config.log. Can you tell me about this error: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC. Does it have something to do with --enable-shared during configuration of fftw, and gromacs? Best Regards, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 6:46:47 PM Subject: Re: [gmx-users] Gromacs Installation majid hasan wrote: Okay, I'll try with --enable-single. But as far as I understood, it seems like its an issue with --enable-shared. In the first attempt, I did enable-shared in fftw configuration, but didn't do it in gromacs configuration, and got this error. In the second attempt, I did enable-shared in ./configure for both fftw and gromacs, but still got the same message. In the third attempt, I didn't enable shared anywhere, and installation went well. Only issue is that when I run ngmx, it says command not found, and I can't view .trr file, but this seems to be a different issue. But I don't know why --enable-shared isn't working. About installing in home directory: actually I downloaded the source from gromacs website, and I did manage to install it in my home directory. But some of the commands, like luck, and ngmx are missing. When I type any of luck, I get, command not found and you can install it by typing sudo apt-get install gromacs. I did try to download it using apt-get and software center in ubuntu, but it installs it in usr/share/gromacs, but I want to install it in my home directory. In the latest version of Gromacs, luck is named g_luck. If ngmx was not installed, then probably the required X11 libraries were not found on your system. Check the output from configuration (i.e. config.log) for details. -Justin Thanks, Majid *From:* lina zhao lnzha...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Mon, February 14, 2011 6:24:47 PM *Subject:* Re: [gmx-users] Gromacs Installation 1. Seems the default fftw configuration is double, when you install the fftw-3.2.2 configure with --enable single. 2. about your question:I wanted to ask if I can download gromacs in my home directory using the ubuntu software center or synaptic manager? 1] You can download in your home directory and install. 2] a better but a bit not so-easy way, is download the source (http://packages.debian.org/sid/gromacs), built the package and add it into repository. There maybe also some other ways. HTH, lina On Tue, Feb 15, 2011 at 6:23 AM, majid hasan pu_majidha...@yahoo.com mailto:pu_majidha...@yahoo.com wrote: Dear All, I am trying to install gromacs in ubuntu. I configured both fftw and gromacs in my home folder following the instructions on http://www.gromacs.org/Downloads/Installation_Instructions. However, when I do make, I get an error in the end (pasted below). I have also attached the log file of compilation with the email. /usr/bin/ld: /home/majid/user/soft/fftw/lib/libfftw3f.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /home/majid/user/soft/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.lahttp://libmd.la] Error 1 make[3]: Leaving directory `/home/majid/user/down/gromacs/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/majid/user/down/gromacs/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/majid/user/down/gromacs/src' make: *** [all-recursive] Error 1 Moreover, I wanted to ask if I can download gromacs in my home directory using the ubuntu software center or synaptic manager? Thanks, Majid Never miss an email again! Yahoo! Toolbar http://us.rd.yahoo.com/evt=49938/*http://tools.search.yahoo.com/toolbar/features/mail/ alerts you the instant new Mail arrives. Check it out. http://us.rd.yahoo.com/evt=49937/*http://tools.search.yahoo.com/toolbar/features/mail/ -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation
Okay. Actually, second time, I over-worte the first installation. I mean I didn't uninstall the first one, I just ran the whole process again starting from fftw$./configure. I am not sure if that is all right, I just did it to find out the problem. In the third attempt (without issuing --enable-shared anywher), I again over-wrote the gromacs installation files, and this went well. It worked, but I don't know why? Best, Majid From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 8:04:38 PM Subject: Re: [gmx-users] Gromacs Installation You are right, it's relevant to the shared libs. but I don't know why you failed in the second attempt if you did a clean reinstallation. lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation
Okay, I'll do this. I have also realized after browsing through config.log, that Xlib.h is absent. Where do I get it, I want it to run ngmx. Thanks, Majid From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 9:07:15 PM Subject: Re: [gmx-users] Gromacs Installation clean reinstallation. make uninstall make distclean rm -r the untar one from source re-install it again. lina On Tue, Feb 15, 2011 at 12:39 PM, majid hasan pu_majidha...@yahoo.com wrote: Okay. Actually, second time, I over-worte the first installation. I mean I didn't uninstall the first one, I just ran the whole process again starting from fftw$./configure. I am not sure if that is all right, I just did it to find out the problem. In the third attempt (without issuing --enable-shared anywher), I again over-wrote the gromacs installation files, and this went well. It worked, but I don't know why? Best, Majid From: ZHAO Lina lnzha...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Mon, February 14, 2011 8:04:38 PM Subject: Re: [gmx-users] Gromacs Installation You are right, it's relevant to the shared libs. but I don't know why you failed in the second attempt if you did a clean reinstallation. lina Don't get soaked. Take a quick peek at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Output of Gromacs Demo
I have attached the output of demo, and another Okay, I just ran the demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here is what I got. You seem to have the DISPLAY variable is set, so we will pop up a window with the output of the pdb2gmx program Press enter Starting pdb2gmx [1] 28221 output.pdb2gmx: Permission denied pdb2gmx finished Press enter### [1]Done xterm -title pdb2gmx -sb -e tail +0f Then it ran genbox, gompp, and mdrun in the end (I am not totally sure of it as I forgot the whole list of programs, if you need complete list, let me know, and I'll post it). I got similar output after every program. I also ran the files from tutor/water folder, but I got the Permission denied message. Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. http://tools.search.yahoo.com/toolbar/features/mail/ demo_contents_1.odt Description: application/vnd.oasis.opendocument.text -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Fw: [gmx-users] Output of Gromacs Demo
I have attached the output of demo, and water with the message. I just ran the demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here is what I got. You seem to have the DISPLAY variable is set, so we will pop up a window with the output of the pdb2gmx program Press enter Starting pdb2gmx [1] 28221 output.pdb2gmx: Permission denied pdb2gmx finished Press enter### [1]Done xterm -title pdb2gmx -sb -e tail +0f Then it ran genbox, gompp, and mdrun in the end (I am not totally sure of it as I forgot the whole list of programs, if you need complete list, let me know, and I'll post it). I got similar output after every program. I also ran the files (conf.gro, topol.top) from tutor/water folder, but I got the Permission denied message. ubuntu:/usr/share/gromacs/water/./conf.gro ./conf.gro: Permission denied I got same output for other files like topol.top etc. Thanks, Majid Looking for earth-friendly autos? Browse Top Cars by Green Rating at Yahoo! Autos' Green Center. TV dinner still cooling? Check out Tonight's Picks on Yahoo! TV. http://tv.yahoo.com/ demo_contents_1.odt Description: application/vnd.oasis.opendocument.text -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Output of Gromacs Demo
Thanks, Justin! Sudo seems to have solved my problem, I do get the outputs now. Best, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sun, February 13, 2011 9:30:52 AM Subject: Re: [gmx-users] Output of Gromacs Demo majid hasan wrote: I have attached the output of demo, and another Okay, I just ran the demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here is what I got. You seem to have the DISPLAY variable is set, so we will pop up a window with the output of the pdb2gmx program Press enter Starting pdb2gmx [1] 28221 output.pdb2gmx: Permission denied pdb2gmx finished Press enter### [1]Done xterm -title pdb2gmx -sb -e tail +0f Then it ran genbox, gompp, and mdrun in the end (I am not totally sure of it as I forgot the whole list of programs, if you need complete list, let me know, and I'll post it). I got similar output after every program. I also ran the files from tutor/water folder, but I got the Permission denied message. If you installed Gromacs in the default location (/usr/local/gromacs) you need administrative privileges to write files to this directory and any subdirectory of it. Thus either issue the demo commands as sudo or install Gromacs elsewhere. Note, too, that there are plenty of other tutorials for learning Gromacs in addition to the demo: http://www.gromacs.org/Documentation/Tutorials -Justin Looking for earth-friendly autos? Browse Top Cars by Green Rating http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI- at Yahoo! Autos' Green Center. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Output of Gromacs Demo
Okay, thanks. I will install it again in some other directory. Majid From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Sun, February 13, 2011 1:39:16 PM Subject: Re: [gmx-users] Output of Gromacs Demo majid hasan wrote: Thanks, Justin! Sudo seems to have solved my problem, I do get the outputs now. You normally don't want to do any work within the Gromacs installation directories. For the demo, I suppose it's alright, but sudo is really just a work-around to write in directories which normally ought not be altered. Note that there are several problems and some of the examples probably won't work. I've fixed these for the next release. gmxdemo should work, but others may not. -Justin Best, Majid *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Sun, February 13, 2011 9:30:52 AM *Subject:* Re: [gmx-users] Output of Gromacs Demo majid hasan wrote: I have attached the output of demo, and another Okay, I just ran the demo and kept pressing enter whenever it asked me. Demo ran the pdb2gmx first, and here is what I got. You seem to have the DISPLAY variable is set, so we will pop up a window with the output of the pdb2gmx program Press enter Starting pdb2gmx [1] 28221 output.pdb2gmx: Permission denied pdb2gmx finished Press enter### [1]Done xterm -title pdb2gmx -sb -e tail +0f Then it ran genbox, gompp, and mdrun in the end (I am not totally sure of it as I forgot the whole list of programs, if you need complete list, let me know, and I'll post it). I got similar output after every program. I also ran the files from tutor/water folder, but I got the Permission denied message. If you installed Gromacs in the default location (/usr/local/gromacs) you need administrative privileges to write files to this directory and any subdirectory of it. Thus either issue the demo commands as sudo or install Gromacs elsewhere. Note, too, that there are plenty of other tutorials for learning Gromacs in addition to the demo: http://www.gromacs.org/Documentation/Tutorials -Justin Looking for earth-friendly autos? Browse Top Cars by Green Rating http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI- at Yahoo! Autos' Green Center. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Expecting? Get great news right away with email Auto-Check. http://us.rd.yahoo.com/evt=49982/*http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html Try the Yahoo! Mail Beta. http://us.rd.yahoo.com/evt=49982/*http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support
[gmx-users] Output of Gromacs Demo
Dear All, I installed the gromacs on Ubuntu, and ran the demo. But every time it produces an output file, I get this error: output.pdb2gmx: Permission denied., so I can't view the output. I am also unable to locate the .trr file, which is supposed to be the ultimate output of demo. Could anyone please tell me what do I have to do avoid this error, and how do I get to .trr file? Thanks, Majid Need Mail bonding? Go to the Yahoo! Mail QA for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=listsid=396546091-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Problem with Gromacs Installation
Dear All, I installed gromacs-4.5.3 using cygwin on windows 7, following the instructions on http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO. However, after installation, when I tried to run gromacs, I couldn't find the share folder in D:/cygwin/usr/local/gromacs. This share folder contains the demo that I was trying to run. I only see bin, include, and lib folders in gromacs. Could anyone please help me with this? Thanks, Majid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
