[gmx-users] Fatal error: Atomtype O2 not found
hi am working on a DNA-protein complex, during the energy minimization step its giving the following error, Fatal error: Atomtype O2 not found am using charmm27 force field and used the command grompp -f minim.mdp -c protein.gro -p protein.top -o protein-EM-vacuum.tpr regards, ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Fatal error: Atomtype O2 not found
On 6/9/12 7:24 AM, ramaraju801 wrote: hi am working on a DNA-protein complex, during the energy minimization step its giving the following error, Fatal error: Atomtype O2 not found am using charmm27 force field and used the command grompp -f minim.mdp -c protein.gro -p protein.top -o protein-EM-vacuum.tpr How did you produce the topology? Did you modify it in any way? As the error message states, O2 is not a valid atom type for CHARMM27. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: Fatal error: Atomtype O2 not found
yes, when creating the topology file i added atom O2 to the .rtp file when it said atom O2 is missing in atomstype regards, ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998256.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Fatal error: Atomtype O2 not found
correction i added O2 atom to atomtypes.atp file regards, ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998257.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Fatal error: Atomtype O2 not found
On 9/06/2012 10:30 PM, ramaraju801 wrote: yes, when creating the topology file i added atom O2 to the .rtp file when it said atom O2 is missing in atomstype Adding O2 to any file is an effective solution. You need to fix your termini properly, by using pdb2gmx -ter or the contents of your coordinate file. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Fatal error: Atomtype O2 not found
On 6/9/12 8:30 AM, ramaraju801 wrote: yes, when creating the topology file i added atom O2 to the .rtp file when it said atom O2 is missing in atomstype It would be useful to show us what you're doing and explain what you're attempting. But the answer remains the same - you cannot use atom types that don't exist. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] Re: Fatal error: Atomtype O2 not found
On 6/9/12 8:31 AM, ramaraju801 wrote: correction i added O2 atom to atomtypes.atp file The atomtypes.atp file is only used by pdb2gmx to make sure it can write certain atom types. If you're introducing a new atom type, its parameters need to go in ffnonbonded.itp, and if it is involved in bonded interactions, those need to go in ffbonded.itp. Before doing all that, you should determine whether all that effort is needed. Based on the information at hand, I am still not clear on why you think the addition is necessary. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: Fatal error: Atomtype O2 not found
@ Mark, i added -ter to pdb2gmx command and produced the topology file but still the energy minimization step in vacuum is producing the same error @justin am presently running the simulation step i.e energy minimization of structure in vacuum. when producing the topology file ,it gave errors saying some of the atoms are missing in atomtypes which i gave , you said atoms shouldn't be added which were not in the first place then can u tell me the alternative. regards ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998261.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Fatal error: Atomtype O2 not found
On 6/9/12 8:53 AM, ramaraju801 wrote: @ Mark, i added -ter to pdb2gmx command and produced the topology file but still the energy minimization step in vacuum is producing the same error @justin am presently running the simulation step i.e energy minimization of structure in vacuum. when producing the topology file ,it gave errors saying some of the atoms are missing in atomtypes which i gave , you said atoms shouldn't be added which were not in the first place then can u tell me the alternative. Not without the exact error, copied and pasted from the terminal. If you're working with a simple protein with canonical amino acids, changing an .rtp file (or anything else in the force field) is never required. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: Fatal error: Atomtype O2 not found
as i said my system is an protein-DNA complex and the error popped up only for atoms in DNA residues. -ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998263.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Fatal error: Atomtype O2 not found
On 9/06/2012 11:08 PM, ramaraju801 wrote: as i said my system is an protein-DNA complex and the error popped up only for atoms in DNA residues. That's about 1% of the detail you'll need to provide in order for it to be worth any more of anybody's time helping you :-) See http://www.gromacs.org/Support for advice on how to effectively ask for help. A complete description of your system contents, and copied and pasted input and output is essential. You already know from past threads that your termini are an issue, so make sure you focus on those details. 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] Re: Automated Topology Builder job partially completed
Justin, I have also question about inclussion of the part of the topology file wich was done by the external server ( e.g by ATB) in the topology of my molecule. E.g I'm working with GFP wich include non-standart chromophore group wich is covalent bonded to the all protein. So I've extracted chromophore only from my GFP and done it parametrisation by ATB. What is the easiliest way to include this new topology as well as part of the molecule back to the whole GFP? Thanks, James 2012/6/8 nore...@compbio.biosci.uq.edu.au Dear Novikov Gleb, Your job that was submitted at 2012-06-09 03:08:37 (RNME = _MAZ) has now partially completed. Initial results are available herehttp://compbio.biosci.uq.edu.au/atb/download.py?session=5194 . Thank you! -- 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] Re: Automated Topology Builder job partially completed
On 6/9/12 10:30 AM, James Starlight wrote: Justin, I have also question about inclussion of the part of the topology file wich was done by the external server ( e.g by ATB) in the topology of my molecule. E.g I'm working with GFP wich include non-standart chromophore group wich is covalent bonded to the all protein. So I've extracted chromophore only from my GFP and done it parametrisation by ATB. What is the easiliest way to include this new topology as well as part of the molecule back to the whole GFP? The only way to do it: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] Re: Fatal error: Atomtype O2 not found
@ram... why dont u post what u did along with the part of the structure/file attached ... and what is the error and what u did to rectify... and as per as i know, if u are working with DNA system along with CHARMM forcefield, u should be careful with the atom types ... since u haven't mentioned. i think the O2 part is from DNA and adding that atom type in aminoacid file (aminoacid.rtp) may not serve ur purpose please check which part does it belong to ( i think its the temini of DNA) and provide the proper aliases and use it .. Thank u Gurunath On Sat, Jun 9, 2012 at 6:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/06/2012 11:08 PM, ramaraju801 wrote: as i said my system is an protein-DNA complex and the error popped up only for atoms in DNA residues. That's about 1% of the detail you'll need to provide in order for it to be worth any more of anybody's time helping you :-) See http://www.gromacs.org/Support for advice on how to effectively ask for help. A complete description of your system contents, and copied and pasted input and output is essential. You already know from past threads that your termini are an issue, so make sure you focus on those details. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] floating point exception in .xtc file
Thank you Mark and Francesco, I have repaired the trajectory and only lost 2 frames (40 ps total lost of 500 ns). I used to automate a gmxcheck of each .xtc segment generated with mdrun -noappend and rerun segments that were corrupted ... I may go back to that usage in the future. For completeness, I believe that the filesystem that we are using is capable of locking files because once and a while after a cluster crash I end up unable to restart simulations because the .log file is locked. In those cases, I do revert back to -noappend for continuations as simply deleting the .log file also makes it impossible to continue the run. Thank you, Chris. -- original message -- Hi Christopher, you can try to use the program gmx_rescue, by Marc Baaden to recovery your trajectory. Below there is the adderess: http://baaden.free.fr/soft/compchem.html Francesco 2012/6/9 Mark Abraham Mark.Abraham at anu.edu.auhttp://lists.gromacs.org/mailman/listinfo/gmx-users On 9/06/2012 7:27 AM, Christopher Neale wrote: Dear Users: I have a 500 ns trajectory of 65 GB that gives a floating point exception when I run it through gmxcheck or trjcat (generated and analyzed with gromacs 4.5.5). Has anybody encountered this? I ran mdrun with -append so this is the xtc resulting from months of simulation of a 1,000,000 atom system. If I run trjconv -f md.xtc -b 20, where the floating point exception occurred around t=18 ps in gmxcheck, then I can extract the readable frames and repair around the damaged section. Still, I'd rather not lose any data and I had thought that the new default -append option to mdrun checked for these types of problems at runtime. I've no idea what might happen when some file-system transient occurs mid-simulation, but if mdrun has managed to compute a checksum on an incomplete file and stored that in the checkpoint, then the append mechanism can be none the wiser. The check upon restart is that the checksum matches, not that the checksum is computed on a file whose properties would satisfy gmxcheck. Note also that some file systems that do not support file locking and this is known to cause issues (Redmine 924), but I don't know if this is related to your observation. 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] g_msd and MSD analysis
Hi everyone! I have a 20 ns simulation (2fs timestep but coordinates saved every 0.2 ps) and I was able to calculate the mean-square-displacement of the oxygen atoms of my water solvent. The entire MSD plot looks very linear to me. I need to fit this set of MSD data to obtain the diffusion coefficient. However, I am not sure if I will have to use the entire MSD points or may be just to consider a few picoseconds at the latter part of the simulation time. In papers I have read, they use up to a 100 ps, although no mention were made as to where those set of points came from. Please help. This post seems to suggest a nanosecond window for the analysis of the MSD curve http://lists.gromacs.org/pipermail/gmx-users/2012-January/067487.html Although, this other one suggests using the latter 40 ps of his MSD http://lists.gromacs.org/pipermail/gmx-users/2009-November/046990.html Your help is greatly appreciated. Thanks, Bernard-- 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
