Re: [gmx-users] DNA not wrapping around CNT in MD simulation
Thanks, I am going through literature at the moment. Any suggestions about tutorials, I don't find much related to it on gromacs? Thanks again, Majid From: Mark Abraham To: Discussion list for GROMACS users Sent: Fri, April 22, 2011 5:45:22 PM Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation On 4/23/2011 9:21 AM, 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. > > >Movie of output is here: >http://phas.ubc.ca/%7Emajid/Project/msteps/cntdna2000ps.mpg >and input em.mdp, and md.mdp files are here: >EM: http://phas.ubc.ca/%7Emajid/Project/msteps/lbfgs.mdp >MD: http://phas.ubc.ca/%7Emajid/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. > > You're still not following a sound equilibration protocol. The velocities you generate at the start are only roughly correct, and your density is probably a bit off. Check out some tutorials, and published work on similar systems. You also need to consider how far apart these species are. If the driving force is electrostatic, the forces drop off as 1/r^2, so you can wait a long time for those to act over a few nanometers, while re-organizing the solvent between them. In real biochemical systems, one doesn't normally observe a single pair of interacting species mate up smoothly. There's a whole pile of things that have to happen, and each successful binding probably results from very many failed attempts. Having many such pairs over longer periods of times means that statistically the events do happen, but that's no good to you if you can only simulate a single pair in a short period. Mark Thanks, >Majid > > From: Justin A. Lemkul >To: Gromacs Users' List >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 >> *To:* Discussion list for GROMACS users >> *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 try
Re: [gmx-users] DNA not wrapping around CNT in MD simulation
Okay, thanks, I'll try longer simulations. Majid From: Justin A. Lemkul To: Gromacs Users' List 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.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 > > <http://phas.ubc.ca/~majid/Project/msteps/md.mdp>I 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 > *To:* Gromacs Users' List > *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 mailto:jalem...@vt.edu>> > > *To:* Discussion list for GROMACS users <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 <mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au ><mailto:mark.abra...@anu.edu.au>>> > > > *To:* Discussion list for GROMACS users <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org>>> > > > *Sent:* Fri, April 22, 2011 1:51:47 AM > > > *S
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 To: Gromacs Users' List 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 > *To:* Discussion list for GROMACS users > *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 <mailto:mark.abra...@anu.edu.au>> > > *To:* Discussion list for GROMACS users <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
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 To: Discussion list for GROMACS users 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 > *To:* Discussion list for GROMACS users > *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
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 To: Discussion list for GROMACS users 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
[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 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 To: Gromacs Users' List 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 > *To:* Gromacs Users' List > *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 mailto:jalem...@vt.edu>> > > *To:* Discussion list for GROMACS users <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-
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 To: Gromacs Users' List 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 > *To:* Discussion list for GROMACS users > *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 &
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 To: Discussion list for GROMACS users 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
[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
Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt
Okay, thanks a lot. Majid From: Justin A. Lemkul To: Gromacs Users' List 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 > *To:* Discussion list for GROMACS users > *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
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 To: Discussion list for GROMACS users 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
[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] atomname2type.n2t file for CNT in amber99
Yea, sure, thanks. Majid From: Justin A. Lemkul To: Gromacs Users' List 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 > *To:* Gromacs Users' List > *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 mailto:jalem...@vt.edu>> > > *To:* Discussion list for GROMACS users <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, 5&6 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<http://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
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 To: Gromacs Users' List 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 > *To:* Discussion list for GROMACS users > *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, 5&6 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<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> > 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
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 To: Discussion list for GROMACS users 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, 5&6 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
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 To: Discussion list for GROMACS users 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, 5&6 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
[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, 5&6 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] 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 To: Discussion list for GROMACS users 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
[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] .top file for DNA-CNT
Okay, thanks, I'll stick to Amber then. Thanks again, Majid From: Justin A. Lemkul To: Gromacs Users' List 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 > *To:* Discussion list for GROMACS users > *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 [sy
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 To: Discussion list for GROMACS users 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
[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] genbox output taking forever to complete
Alright, thanks. Majid From: Justin A. Lemkul To: Gromacs Users' List 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
Re: [gmx-users] genbox output taking forever to complete
Okay, thank you. Majid From: Justin A. Lemkul To: Gromacs Users' List 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 0While solvent and DNA atoms are in the region 4 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
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 0 To: Gromacs Users' List 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 > *To:* Gromacs Users' List > *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<http://vt.edu> | (540) 231-9080 > http://www.bevanlab.biochem.vt.
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 To: Gromacs Users' List 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, thanks Justin!. Majid From: Justin A. Lemkul To: Gromacs Users' List 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
[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] Dangling bond error for dna
Okay, I am trying AmberTools as well. Thanks Justin! Majid From: Justin A. Lemkul To: Gromacs Users' List 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 > *To:* Gromacs Users' List > *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<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> > 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] 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 To: Gromacs Users' List 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, thank you. I'll try to fix it. Majid From: Justin A. Lemkul To: Gromacs Users' List 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
.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 To: Discussion list for GROMACS users 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] 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] Naming of DNA residues, and structure of .pdb file
Okay, thanks a lot. Majid From: Justin A. Lemkul To: Discussion list for GROMACS users 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] Naming of DNA residues, and structure of .pdb file
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? 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? Thanks, Majid ssdna.pdb 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
Oh, yes, I could open it in text editor. I didn't realize that. Thanks, Majid From: Justin A. Lemkul To: Gromacs Users' List Sent: Fri, April 8, 2011 6:48:13 PM Subject: Re: [gmx-users] .n2t file for ssDNA majid hasan wrote: > I looked at the error in more detail (output attached), and it says that: >Warning: Residue T6 in chain has different type (Other) from starting residue >A1 >(RNA). I had a dna.pdb file so first but its reading the first residue as RNA. > > So to me, problem seems to be that residues are named differently in my > dna.pdb >file and dna.rtp file of force field. I looked at dna.pdb file using more >dna.pdb (output attached), and the residues are named as A, C, G, T, while in >Amber's dna.rtp file (attached) these are named as DA3, DC3. Could this be a >problem? If this is, then how do I change the names of residues in .pdb file, >which I created it using a different software (3DNA, and Gabedit)? > The names of the residues must conform to the names found in the force field .rtp file. The changes can be made with a text editor, but be careful not to shift the spacing of the .pdb file; its format must remain fixed. -Justin > 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] .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 To: Gromacs Users' List 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 > *To:* Gromacs Users' List > *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 mailto:jalem...@vt.edu>> > > *To:* Discussion list for GROMACS users <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.edu<http://vt.edu> <
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 To: Gromacs Users' List 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 > *To:* Discussion list for GROMACS users > *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<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> > 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
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 To: Discussion list for GROMACS users 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
[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
[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 To: Discussion list for GROMACS users 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 >To: Discussion list for GROMACS users >Sent: Mon, February 14, 2011 9:07:15 PM >Subject: Re: [gmx-users] Gromacs Installation > >"clean" reinstallation. > >make uninstall >make distclean >rm -r > >from source re-install it again. > >lina > > >On Tue, Feb 15, 2011 at 12:39 PM, majid hasan > 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$./configure. I am not sure if that is all right, I >just did it to find out the problem. In the third >attempt >(without issuing --enable-shared anywher), I again >over-wrote the gromacs installation files, and this went >well. It worked, but I don't know why? >> >> >>Best, >>Majid >> >> >> From: ZHAO Lina >> >>To: Discussion list for GROMACS users >>Sent: Mon, February 14, 2011 8:04:38 PM >> >>Subject: Re: [gmx-users] Gromacs Installation >> >> >>You are right, it's relevant to the shared libs. >>but I don't know why you failed in the second >>attempt >>if you did a clean reinstallation. >> >>lina >> >> >> >> >> > Food fight? Enjoy some healthy debate >in the Yahoo! Answers Food & Drink Q&A. No need to miss a message. Get email on-the-go with Yahoo! Mail for Mobile. Get started. http://mobile.yahoo.com/mail -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs Installation
Okay, I'll do this. I have also realized after browsing through config.log, that Xlib.h is absent. Where do I get it, I want it to run ngmx. Thanks, Majid From: ZHAO Lina To: Discussion list for GROMACS users Sent: Mon, February 14, 2011 9:07:15 PM Subject: Re: [gmx-users] Gromacs Installation "clean" reinstallation. make uninstall make distclean rm -r from source re-install it again. lina On Tue, Feb 15, 2011 at 12:39 PM, majid hasan wrote: Okay. Actually, second time, I over-worte the first installation. I mean I didn't uninstall the first one, I just ran the whole process again starting from fftw$./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 > >To: Discussion list for GROMACS users >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] 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 To: Discussion list for GROMACS users 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, 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 To: Discussion list for GROMACS users 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 > *To:* Discussion list for GROMACS users > *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 <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.la<http://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@grom
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 To: Discussion list for GROMACS users 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 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
[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] Output of Gromacs Demo
Okay, thanks. I will install it again in some other directory. Majid From: Justin A. Lemkul To: Gromacs Users' List 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 > *To:* Discussion list for GROMACS users > *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 > > Starting pdb2gmx > > [1] 28221 > > output.pdb2gmx: Permission denied > > pdb2gmx finished > > Press >### > > [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<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> > 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.
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 To: Discussion list for GROMACS users 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 > Starting pdb2gmx > [1] 28221 > output.pdb2gmx: Permission denied > pdb2gmx finished > Press >### > [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
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 Starting pdb2gmx [1] 28221 output.pdb2gmx: Permission denied pdb2gmx finished Press ### [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
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 Starting pdb2gmx [1] 28221 output.pdb2gmx: Permission denied pdb2gmx finished Press ### [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
[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 Q&A for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=list&sid=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
