[gmx-users] RE: Position restraints
Thank you for responce and explanation! So is it a good alghorithm to use gromacs genrestr command and then include this posre.itp file into topology (without any changes) after insertion of a ligand.itp? Thank you in advance On 4/2/13 6:07 AM, alex rayevsky wrote: Dear All! I have a doubt about the rightness of ligand/molecule integration in the topology file. I'm using an amber (tleap) or swissparam.ch to build a topology of the residue (modified trna). Is it neccessary to generate a position restrain file (genrestr program) for this residue or not? I've started both dynamics with/without posrestraints on my residue, however I'm really not sure that my results from both of them are different. But I want to do everything in right way, so what can you say about this? Restraints during equilibration are used to prevent unnatural forces from theunequilibrated solvent and help prevent deformation of the structure. It's never a bad idea to restrain the whole solute. If I were reading a paper thatdescribed restraining the whole solute, except for one residue because it wasspecial or difficult to deal with, I would immediately be suspicious. -Justin -- * Nemo me impune lacessit* -- 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: density profile
On Wed, Apr 3, 2013 at 4:56 AM, Elisabeth katesed...@gmail.com wrote: Hi Vitaly, I realize that when one extends the Z direction the resulting interface is liquid-vacuum, but I see that even at T below boiling point some molecules still leave the interface and enter the empty zone and are added to the other side due to PBC. as a result the density profile does not exactly go down to zero but tends to zero anyways. I was wondering if this is considered a liquid-vapor interface? YES or it is still liquid-vacuum? thanks! On 1 April 2013 14:43, Dr. Vitaly Chaban vvcha...@gmail.com wrote: There is a wonderful data page devoted to methane in wikipedia... It follows from this webpage that you will get a perfect density profile if you decrease your T down to 150K... On Mon, Apr 1, 2013 at 8:37 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth katesed...@gmail.com wrote: You are right. I compressed my alkane system under NPT at 400 K at 100 bar. The normal boiling point is below 425 K. So it seems there in no way one can obtain profiles obove boiling point of liquid given than with the current NVT recipe molecules tend to fill up the free zone no matter how much pressure was applied in the previous NPT runs? You cannot get a profile just because you have NO LIQUID and NO INTERFACE upon these conditions. Gas fills all the available space, there is no such thing as gas/gas interface. And yeah... Forget about NPT and learn the Gibbs phase rule. Dr. Vitaly Chaban On 1 April 2013 14:22, Dr. Vitaly Chaban vvcha...@gmail.com wrote: On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth katesed...@gmail.comwrote: Hi Vitaly, The problem was with cpt file since it re sets the last line of gro. I removed the -f flag and now the Z direction is extended. However, I see that molecules tend to fill up the upper zone (free space) rapidly. I am wondering how I can obtain the density profile if I am going to get another uniformly distributed box after this NVT run? Here we come to the question what your system is composed of... Based on the density profile, this is not a (conventional) liquid... Polymer, non-Newtonian liquid ... or what? If molecules tend to fill vacuum, it can only mean that the matter you are simulating is above critical point. What is your T and what are the particles in your box? Dr. Vitaly Chaban I am expecting to see how density changes with Z at the solvent -vacuum interface Please advise me on this,, Thanks! On 1 April 2013 13:14, Dr. Vitaly Chaban vvcha...@gmail.com wrote: I think if you use checkpoint files, the program does not read either MDP, or GRO, or TOP, or anything except CPT. Dr. Vitaly Chaban On Mon, Apr 1, 2013 at 7:10 PM, Elisabeth katesed...@gmail.comwrote: Hi vitaly, The initial structure is indeed extended but the final output.gro is not. I think its because I am using the cpt file from the previous NPT runs as input for the new runs? Do I have to remove the -t flag? On 1 April 2013 12:47, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Hi Elisabeth - The only explanation is that you actually DID NOT extend the box in Z direction. Look at the last line of confout.gro. g_density -d Z gives you a [local] density versus Z coordinate. Dr. Vitaly Chaban On Mon, Apr 1, 2013 at 5:33 PM, Elisabeth katesed...@gmail.comwrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- 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: gromacs 4.6.1 on win7?
Dear gmx, I have tried in both (32 and 64 bit cygwin) format in my win7 -64 bit system but both gave me the compiler gcc-broken as follows : -- Check for working C compiler: /usr/bin/gcc-4.exe -- broken (32 bit) -- Check for working C compiler: /usr/bin/gcc.exe -- broken (64 bit) -- 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] g_hbond
Yes. On 3 Apr 2013, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I am calculating the hydrogen bond life time for my system. Do program consider the hydrogen bond criteria for calculation of autocorrelation function? Nilesh -- 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] water models tip3p.gro and spce.gro
Dear users, I will run MD simulations of all water models in Gromacs. I need spce.gro and tip3p.gro files. How can I find them? Thanks in advance -- Ahmet Yıldırım -- 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: Position restraints
On 4/3/13 2:36 AM, alex rayevsky wrote: Thank you for responce and explanation! So is it a good alghorithm to use gromacs genrestr command and then include this posre.itp file into topology (without any changes) after insertion of a ligand.itp? As long as you use a suitable input file for genrestr, e.g. the ligand only. Numbering in the position restraint .itp file is based on [moleculetype], so if you use a coordinate file that has multiple molecules in it when running genrestr, it won't work. -Justin Thank you in advance On 4/2/13 6:07 AM, alex rayevsky wrote: Dear All! I have a doubt about the rightness of ligand/molecule integration in the topology file. I'm using an amber (tleap) or swissparam.ch to build a topology of the residue (modified trna). Is it neccessary to generate a position restrain file (genrestr program) for this residue or not? I've started both dynamics with/without posrestraints on my residue, however I'm really not sure that my results from both of them are different. But I want to do everything in right way, so what can you say about this? Restraints during equilibration are used to prevent unnatural forces from theunequilibrated solvent and help prevent deformation of the structure. It's never a bad idea to restrain the whole solute. If I were reading a paper thatdescribed restraining the whole solute, except for one residue because it wasspecial or difficult to deal with, I would immediately be suspicious. -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] water models tip3p.gro and spce.gro
On 4/3/13 6:26 AM, Ahmet yıldırım wrote: Dear users, I will run MD simulations of all water models in Gromacs. I need spce.gro and tip3p.gro files. How can I find them? These don't exist within Gromacs. Since SPC, SPC/E, and TIP3P are all 3-point water molecules, just use spc216.gro and equilibrate using the desired model. -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] 1-4 interactions
After reading the manual and trying to find more information on the mailing list. I'm still not sure about this 1-4 interactions, when I want to calculate the energy between two groups (lets say one residue and the rest of the protein) should I sum everything (including the 1-4 interactions) or should I only include the SR interactions. Thank you! Liron -- 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] 1-4 interactions
On 4/3/13 7:16 AM, Liron Cohen wrote: After reading the manual and trying to find more information on the mailing list. I'm still not sure about this 1-4 interactions, when I want to calculate the energy between two groups (lets say one residue and the rest of the protein) should I sum everything (including the 1-4 interactions) or should I only include the SR interactions. 1-4 interactions are intramolecular and thus should not be included in intermolecular energies. If you're using PME, decomposing the long-range component to the electrostatics term is challenging. -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] 1-4 interactions
I am using PME, can you elaborate about the decomposing you mentioned? From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, April 03, 2013 2:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] 1-4 interactions On 4/3/13 7:16 AM, Liron Cohen wrote: After reading the manual and trying to find more information on the mailing list. I'm still not sure about this 1-4 interactions, when I want to calculate the energy between two groups (lets say one residue and the rest of the protein) should I sum everything (including the 1-4 interactions) or should I only include the SR interactions. 1-4 interactions are intramolecular and thus should not be included in intermolecular energies. If you're using PME, decomposing the long-range component to the electrostatics term is challenging. -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 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] 1-4 interactions
On 4/3/13 7:49 AM, Liron Cohen wrote: I am using PME, can you elaborate about the decomposing you mentioned? The mesh term includes all long-range interactions and is not broken down, even in the presence of energygrps in the .mdp file. Some time ago, someone posted a method of several re-runs with custom .tpr files that suggested one could determine the individual contributions of different molecules to the mesh, but I don't know if anyone ever tried it or if it would even work. People often measure these so-called interaction energies, and they can be useful in some cases, but no force field has ever been parametrized to guarantee that such a number would even make sense. Interaction energies may provide some qualitative insight, but if you want real quantitative metrics of interaction strength, you should probably be doing real free energy calculations. -Justin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, April 03, 2013 2:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] 1-4 interactions On 4/3/13 7:16 AM, Liron Cohen wrote: After reading the manual and trying to find more information on the mailing list. I'm still not sure about this 1-4 interactions, when I want to calculate the energy between two groups (lets say one residue and the rest of the protein) should I sum everything (including the 1-4 interactions) or should I only include the SR interactions. 1-4 interactions are intramolecular and thus should not be included in intermolecular energies. If you're using PME, decomposing the long-range component to the electrostatics term is challenging. -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 -- 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] Simulation of the HEM-containing proteins
Dear Gromacs users! I want to simulate Cytochrome C in complex with HEM using NMR full-atom structure of that protein as the starting conformation and charm36 force field's parameters. in the charm36 ff I've found parameters for HEM but I have not found params for the hydrogens (in the aminoacids.hdb file) as well as definition of the HEM as the part of the protein in the residuetypes.dat ( including connection to the rest of polypeptide chain ). So during pdb2gmx parametrisation I've obtained errors like WARNING: atom HA is missing in residue HEME 105 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEME 105 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEME 105 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HD is missing in residue HEME 105 in the pdb file You might need to add atom HD to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) Have anybody such missing parameters? James -- 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 the HEM-containing proteins
On Wed, Apr 3, 2013 at 8:24 AM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs users! I want to simulate Cytochrome C in complex with HEM using NMR full-atom structure of that protein as the starting conformation and charm36 force field's parameters. in the charm36 ff I've found parameters for HEM but I have not found params for the hydrogens (in the aminoacids.hdb file) as well as definition of the HEM as the part of the protein in the residuetypes.dat ( including connection to the rest of polypeptide chain ). So during pdb2gmx parametrisation I've obtained errors like WARNING: atom HA is missing in residue HEME 105 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEME 105 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEME 105 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HD is missing in residue HEME 105 in the pdb file You might need to add atom HD to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) Have anybody such missing parameters? There aren't missing parameters, per se. The parameters are all there in the .rtp and other force field files. You just need to construct an .hdb entry for HEM, as pdb2gmx says. See the manual, section 5.6.4. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] Simulation of the HEM-containing proteins
hmm I've done parametrization of the hem using standart charmm36 parameters but indeed there is some confusing with the hydrogens for example my pdb (obtained from NMR structure) consist of 2 extra hydrogens (which both parts of the methyl groups) which are not present in the rtp parameters. So if I delete both of that hydrogens from pdb- my HEM will be -2 charged. On tyhe other hands hem in my pdb lack of 2 protons in the COOH groups. Could someone provide me with the HEM (in planargeometry) parametrized in charmm36 ? By the way assuming that the HEM itself is not covalently bonded to the rest of the protein ( as in the case of GFP or rhodopsin). So the parameters for the hem should be included as the any other diffusiable ligand (as the separate itp file) in topology, should'n it? James 2013/4/3 Justin Lemkul jalem...@vt.edu On Wed, Apr 3, 2013 at 8:24 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I want to simulate Cytochrome C in complex with HEM using NMR full-atom structure of that protein as the starting conformation and charm36 force field's parameters. in the charm36 ff I've found parameters for HEM but I have not found params for the hydrogens (in the aminoacids.hdb file) as well as definition of the HEM as the part of the protein in the residuetypes.dat ( including connection to the rest of polypeptide chain ). So during pdb2gmx parametrisation I've obtained errors like WARNING: atom HA is missing in residue HEME 105 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEME 105 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEME 105 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HD is missing in residue HEME 105 in the pdb file You might need to add atom HD to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) Have anybody such missing parameters? There aren't missing parameters, per se. The parameters are all there in the .rtp and other force field files. You just need to construct an .hdb entry for HEM, as pdb2gmx says. See the manual, section 5.6.4. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] Re: gromacs 4.6.1 on win7?
Does other compiling with these compilers work? Mark On Wed, Apr 3, 2013 at 10:12 AM, 라지브간디 ra...@kaist.ac.kr wrote: Dear gmx, I have tried in both (32 and 64 bit cygwin) format in my win7 -64 bit system but both gave me the compiler gcc-broken as follows : -- Check for working C compiler: /usr/bin/gcc-4.exe -- broken (32 bit) -- Check for working C compiler: /usr/bin/gcc.exe -- broken (64 bit) -- 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] FW: No subject
http://www.satoriholistichealth.com/uws/wd.fto?ntw Wholly Peach 4/3/2013 2:39:18 PM rl 4/3/2013 2:39:18 PM Wholly Peach -- 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 the HEM-containing proteins
sorry it was mistake :) assuming that heme is covalently bonded to the cytochrome by means of 2 cysteines how should I define such bindings (assuming that heme is part of my protein) based onb the charmm parameters ? its not clear for me why such connection is absent in the residue.dat (having HEME included in the rtps) I still need a example of properly parametrized hem complexed with any cytochrome :) James 2013/4/3 James Starlight jmsstarli...@gmail.com hmm I've done parametrization of the hem using standart charmm36 parameters but indeed there is some confusing with the hydrogens for example my pdb (obtained from NMR structure) consist of 2 extra hydrogens (which both parts of the methyl groups) which are not present in the rtp parameters. So if I delete both of that hydrogens from pdb- my HEM will be -2 charged. On tyhe other hands hem in my pdb lack of 2 protons in the COOH groups. Could someone provide me with the HEM (in planargeometry) parametrized in charmm36 ? By the way assuming that the HEM itself is not covalently bonded to the rest of the protein ( as in the case of GFP or rhodopsin). So the parameters for the hem should be included as the any other diffusiable ligand (as the separate itp file) in topology, should'n it? James 2013/4/3 Justin Lemkul jalem...@vt.edu On Wed, Apr 3, 2013 at 8:24 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I want to simulate Cytochrome C in complex with HEM using NMR full-atom structure of that protein as the starting conformation and charm36 force field's parameters. in the charm36 ff I've found parameters for HEM but I have not found params for the hydrogens (in the aminoacids.hdb file) as well as definition of the HEM as the part of the protein in the residuetypes.dat ( including connection to the rest of polypeptide chain ). So during pdb2gmx parametrisation I've obtained errors like WARNING: atom HA is missing in residue HEME 105 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEME 105 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEME 105 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HD is missing in residue HEME 105 in the pdb file You might need to add atom HD to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) Have anybody such missing parameters? There aren't missing parameters, per se. The parameters are all there in the .rtp and other force field files. You just need to construct an .hdb entry for HEM, as pdb2gmx says. See the manual, section 5.6.4. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] Simulation of the HEM-containing proteins
I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but after processing that structure to grompp I've obtained errors like ERROR 1 [file topol.top, line 2106]: No default Bond types ERROR 2 [file topol.top, line 2144]: No default Bond types ERROR 3 [file topol.top, line 3153]: No default Bond types ERROR 4 [file topol.top, line 8725]: No default U-B types ERROR 5 [file topol.top, line 8792]: No default U-B types ERROR 6 [file topol.top, line 10624]: No default U-B types ERROR 7 [file topol.top, line 10625]: No default U-B types ERROR 8 [file topol.top, line 11382]: No default U-B types ERROR 9 [file topol.top, line 11383]: No default U-B types ERROR 10 [file topol.top, line 11384]: No default U-B types ERROR 11 [file topol.top, line 11385]: No default U-B types ERROR 12 [file topol.top, line 11491]: No default U-B types ERROR 13 [file topol.top, line 11492]: No default U-B types ERROR 14 [file topol.top, line 11493]: No default U-B types ERROR 15 [file topol.top, line 11506]: No default U-B types ERROR 16 [file topol.top, line 11507]: No default U-B types ERROR 17 [file topol.top, line 11508]: No default U-B types ERROR 18 [file topol.top, line 12147]: No default Proper Dih. types ERROR 19 [file topol.top, line 12148]: No default Proper Dih. types ERROR 20 [file topol.top, line 12149]: No default Proper Dih. types ERROR 21 [file topol.top, line 12150]: No default Proper Dih. types ERROR 22 [file topol.top, line 12151]: No default Proper Dih. types ERROR 23 [file topol.top, line 12152]: No default Proper Dih. types ERROR 24 [file topol.top, line 12247]: No default Proper Dih. types ERROR 25 [file topol.top, line 12248]: No default Proper Dih. types ERROR 26 [file topol.top, line 12249]: No default Proper Dih. types ERROR 27 [file topol.top, line 12250]: No default Proper Dih. types ERROR 28 [file topol.top, line 12251]: No default Proper Dih. types ERROR 29 [file topol.top, line 12252]: No default Proper Dih. types ERROR 30 [file topol.top, line 14948]: No default Proper Dih. types ERROR 31 [file topol.top, line 14950]: No default Proper Dih. types ERROR 32 [file topol.top, line 14952]: No default Proper Dih. types ERROR 33 [file topol.top, line 14956]: No default Proper Dih. types ERROR 34 [file topol.top, line 14957]: No default Proper Dih. types ERROR 35 [file topol.top, line 14958]: No default Proper Dih. types ERROR 36 [file topol.top, line 14959]: No default Proper Dih. types ERROR 37 [file topol.top, line 14960]: No default Proper Dih. types ERROR 38 [file topol.top, line 14961]: No default Proper Dih. types ERROR 39 [file topol.top, line 14962]: No default Proper Dih. types ERROR 40 [file topol.top, line 14963]: No default Proper Dih. types ERROR 41 [file topol.top, line 14964]: No default Proper Dih. types ERROR 42 [file topol.top, line 14965]: No default Proper Dih. types ERROR 43 [file topol.top, line 14966]: No default Proper Dih. types ERROR 44 [file topol.top, line 16263]: No default Proper Dih. types ERROR 45 [file topol.top, line 16264]: No default Proper Dih. types ERROR 46 [file topol.top, line 16269]: No default Proper Dih. types ERROR 47 [file topol.top, line 16270]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 3 [file topol.top, line 16745]: System has non-zero total charge: 7.01 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. --- Program grompp, VERSION 4.6 Source code file: /home/own/Documents/distr/gromacs-4.6/src/kernel/grompp.c, line: 1593 Fatal error: There were 47 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors During visualization of the complex.gro file I didnt observe any distortions in the geometry of heme-cytochrome complex (it looks like NMR structure) but why that errors occured ? James 2013/4/3 James Starlight jmsstarli...@gmail.com sorry it was mistake :) assuming that heme is covalently bonded to the cytochrome by means of 2 cysteines how should I define such bindings (assuming that heme is part of my protein) based onb the charmm parameters ? its not clear for me why such connection is absent in the residue.dat (having HEME included in the rtps) I still need a example of properly parametrized hem complexed with any cytochrome :) James 2013/4/3 James Starlight jmsstarli...@gmail.com hmm I've done parametrization of the hem using standart charmm36 parameters but indeed there is some confusing with the hydrogens for example my pdb (obtained from NMR structure)
Re: [gmx-users] Simulation of the HEM-containing proteins
On Wed, Apr 3, 2013 at 10:27 AM, James Starlight jmsstarli...@gmail.comwrote: I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but after processing that structure to grompp I've obtained errors like ERROR 1 [file topol.top, line 2106]: No default Bond types ERROR 2 [file topol.top, line 2144]: No default Bond types ERROR 3 [file topol.top, line 3153]: No default Bond types ERROR 4 [file topol.top, line 8725]: No default U-B types ERROR 5 [file topol.top, line 8792]: No default U-B types ERROR 6 [file topol.top, line 10624]: No default U-B types ERROR 7 [file topol.top, line 10625]: No default U-B types ERROR 8 [file topol.top, line 11382]: No default U-B types ERROR 9 [file topol.top, line 11383]: No default U-B types ERROR 10 [file topol.top, line 11384]: No default U-B types ERROR 11 [file topol.top, line 11385]: No default U-B types ERROR 12 [file topol.top, line 11491]: No default U-B types ERROR 13 [file topol.top, line 11492]: No default U-B types ERROR 14 [file topol.top, line 11493]: No default U-B types ERROR 15 [file topol.top, line 11506]: No default U-B types ERROR 16 [file topol.top, line 11507]: No default U-B types ERROR 17 [file topol.top, line 11508]: No default U-B types ERROR 18 [file topol.top, line 12147]: No default Proper Dih. types ERROR 19 [file topol.top, line 12148]: No default Proper Dih. types ERROR 20 [file topol.top, line 12149]: No default Proper Dih. types ERROR 21 [file topol.top, line 12150]: No default Proper Dih. types ERROR 22 [file topol.top, line 12151]: No default Proper Dih. types ERROR 23 [file topol.top, line 12152]: No default Proper Dih. types ERROR 24 [file topol.top, line 12247]: No default Proper Dih. types ERROR 25 [file topol.top, line 12248]: No default Proper Dih. types ERROR 26 [file topol.top, line 12249]: No default Proper Dih. types ERROR 27 [file topol.top, line 12250]: No default Proper Dih. types ERROR 28 [file topol.top, line 12251]: No default Proper Dih. types ERROR 29 [file topol.top, line 12252]: No default Proper Dih. types ERROR 30 [file topol.top, line 14948]: No default Proper Dih. types ERROR 31 [file topol.top, line 14950]: No default Proper Dih. types ERROR 32 [file topol.top, line 14952]: No default Proper Dih. types ERROR 33 [file topol.top, line 14956]: No default Proper Dih. types ERROR 34 [file topol.top, line 14957]: No default Proper Dih. types ERROR 35 [file topol.top, line 14958]: No default Proper Dih. types ERROR 36 [file topol.top, line 14959]: No default Proper Dih. types ERROR 37 [file topol.top, line 14960]: No default Proper Dih. types ERROR 38 [file topol.top, line 14961]: No default Proper Dih. types ERROR 39 [file topol.top, line 14962]: No default Proper Dih. types ERROR 40 [file topol.top, line 14963]: No default Proper Dih. types ERROR 41 [file topol.top, line 14964]: No default Proper Dih. types ERROR 42 [file topol.top, line 14965]: No default Proper Dih. types ERROR 43 [file topol.top, line 14966]: No default Proper Dih. types ERROR 44 [file topol.top, line 16263]: No default Proper Dih. types ERROR 45 [file topol.top, line 16264]: No default Proper Dih. types ERROR 46 [file topol.top, line 16269]: No default Proper Dih. types ERROR 47 [file topol.top, line 16270]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 3 [file topol.top, line 16745]: System has non-zero total charge: 7.01 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. --- Program grompp, VERSION 4.6 Source code file: /home/own/Documents/distr/gromacs-4.6/src/kernel/grompp.c, line: 1593 Fatal error: There were 47 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors During visualization of the complex.gro file I didnt observe any distortions in the geometry of heme-cytochrome complex (it looks like NMR structure) but why that errors occured ? Heme is tricky, and this error comes up every time someone tries to use heme in Gromacs (see the archive for tips and possible solutions). Parameters are missing for bonded interactions, so either add them directly to the .top or to ffbonded.itp. You'll have to search the literature for suitable parameters or derive them yourself. There are lots of reports of heme-containing proteins being simulated, so clearly the fully parameter set exists somewhere. -Justin -- Justin
[gmx-users] Applying periodic boundary conditions in energy minimization
Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess this is because periodic conditions are not applied. My em.mdp file is: ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1000 ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1 rvdw= 1 Tcoupl = no Pcoupl = no gen_vel = no pbc = xyz I used the following commands: grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 2 mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log Can you please tell me what I am doing wrong. Thanks in advance -- 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] Using two integrators in energy minimization
I want to use both steepest descent and conjugate gradient in my energy minimization. I need the system to use steepest descent for a given number of steps and then switch over to conjugate gradient. Can anyone please suggest how I can do this? How should I make the em.mdp file Thanks in advance. -- 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] Using two integrators in energy minimization
On Wed, Apr 3, 2013 at 11:07 AM, Abhinav Agrawal abhv.a...@gmail.comwrote: I want to use both steepest descent and conjugate gradient in my energy minimization. I need the system to use steepest descent for a given number of steps and then switch over to conjugate gradient. Can anyone please suggest how I can do this? How should I make the em.mdp file You make two, one that specifies the steepest descent process, and one that specifies CG. The output of step 1 becomes the input for step 2. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] Applying periodic boundary conditions in energy minimization
On Wed, Apr 3, 2013 at 10:51 AM, Abhinav Agrawal abhv.a...@gmail.comwrote: Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess this is because periodic conditions are not applied. My em.mdp file is: ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1000 ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1 rvdw= 1 Tcoupl = no Pcoupl = no gen_vel = no pbc = xyz This last line means PBC are being applied. Your observations are consistent with using a box that is too small for the solute, but since you haven't supplied information as to (1) what the system is, (2) how you built it, or (3) how large the box is, there's very little to say beyond speculation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] g_dipoles: index group is not a set of the whole molecules
Dear Gromacs users, can you help me please with next issue: I'm analysing solvation shell of water molecules around a protein. I use g_select to select different layers of water based on distance criteria. The output index file contains all the atoms which satisfy the specified criteria. For some molecules on the edge only some atoms are within the specified distance from protein. So some molecules in the selection are represented only by 1 or 2 atoms out of 3. Such selection works fine for example for g_hbond, but it does not work for g_dipoles. The error in case of g_dipoles is: index group is not a set of whole molecules is there a smart way (except manual editing of .ndx file) to select the whole molecules within some distance from protein (with COM within specified distance from protein surface)? thanks, Oleksandr -- 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] Applying periodic boundary conditions in energy minimization
There is no outside of the box. Tsjerk On Wed, Apr 3, 2013 at 4:51 PM, Abhinav Agrawal abhv.a...@gmail.com wrote: Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess this is because periodic conditions are not applied. My em.mdp file is: ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1000 ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1 rvdw= 1 Tcoupl = no Pcoupl = no gen_vel = no pbc = xyz I used the following commands: grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 2 mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log Can you please tell me what I am doing wrong. Thanks in advance -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] Salt bridge observation
Dear users, This is regarding an observation while calculating the salt bridge (sb) using g_saltbr. I used g_saltbr and g_hbond (with contact option) with a cut of of 4Ang, for calculating sb in the whole protein at a single frame. I made sure that I considered sb between same set of residues (ASP, GLU with LYS ARG) in both calculations. and filtered accordingly. While checking the individual sb it was found that most of the results from g_saltbr matches with g_hbond but g_saltbr gives some extra sbs. On checking these extra sb it was found that the distance between the atoms forming sb are more than the cut of I had mentioned (4 Ang). Not sure why it is like this. But just wanted to convey this observation. Thank you regards Kavya -- 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] Salt bridge observation
On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, This is regarding an observation while calculating the salt bridge (sb) using g_saltbr. I used g_saltbr and g_hbond (with contact option) with a cut of of 4Ang, for calculating sb in the whole protein at a single frame. I made sure that I considered sb between same set of residues (ASP, GLU with LYS ARG) in both calculations. and filtered accordingly. While checking the individual sb it was found that most of the results from g_saltbr matches with g_hbond but g_saltbr gives some extra sbs. On checking these extra sb it was found that the distance between the atoms forming sb are more than the cut of I had mentioned (4 Ang). Not sure why it is like this. But just wanted to convey this observation. Please provide a concrete example. Note that running g_saltbr and g_hbond (with the index files mentioned before) should not be expected to produce equivalent result. g_saltbr is relatively stupid; it considers any group with a charge ± 0.2 to be capable of participating in a salt bridge. In some cases, this will include methylene groups or others than are near the actual charged groups. Such behavior could easily account for whatever observation you're making. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] New python package with gromacs support
Hello GMX users, I just wanted to share a python library I made that may be of help to someone. It includes a molecular viewer and native parsing of xtc and edr files. Go check it out! http://chemlab.github.com/chemlab 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] g_dipoles: index group is not a set of the whole molecules
On 4/3/13 11:13 AM, Oleksandr Sushko wrote: Dear Gromacs users, can you help me please with next issue: I'm analysing solvation shell of water molecules around a protein. I use g_select to select different layers of water based on distance criteria. The output index file contains all the atoms which satisfy the specified criteria. For some molecules on the edge only some atoms are within the specified distance from protein. So some molecules in the selection are represented only by 1 or 2 atoms out of 3. Such selection works fine for example for g_hbond, but it does not work for g_dipoles. The error in case of g_dipoles is: index group is not a set of whole molecules is there a smart way (except manual editing of .ndx file) to select the whole molecules within some distance from protein (with COM within specified distance from protein surface)? It would help to know exactly what your selection syntax was. I think you can use something like same residue as (within ...) for your selection, but I haven't tried it. -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] cannot read frames out from trr files
Dear GMX users, I am not sure if someone has similar problems before. I cannot read half of the frames from trr file after md simulation, and I believe my simulation has already completed. I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the only difference between A and B is they are npt simulations under different temperature (in mdp file, ref_t part )and such difference would not cause crash of the simulation. I have successfully finished A, everything looks perfect (frames can be successfully extracted), but for B, I could not extract last 70ns' frames from trr. 1) My command is like: mdrun_mpi -s -deffnm MD_A -cpi -append, because I am using super computer so the job will be restarted for multiple times. 2) both simulation are 100ns, both log files indicate that they have finished 100ns simulations. I checked my screen out put for B, whenever it restarted, the output on screen is correct and continuously ( something like: 1 steps, 10.0 ps (continuing from step 95963500, 95963.5 ps). 3) With gmxcheck, it looks that my B simulation only reached 29,7ns(which means only the first two restart simulation were recorded into trr, which log files are not saying in this way.) * * *For system A (the successful one), it shows* Reading frame 0 time0.000 # Atoms 72166 Last frame 2000 time 10.000 Item#frames Timestep (ps) Step 200150 Time 200150 Lambda 200150 Coords 200150 Velocities 200150 Forces 0 Box200150 *for system B (the failed one)* Reading frame 0 time0.000 # Atoms 72166 Reading frame 500 time 25000.000 Item#frames Timestep (ps) Step 59650 Time 59650 Lambda 59650 Coords 59650 Velocities 59650 Forces 0 Box59650 4) I also compared the generated files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching 100ns, the size would be the same as A. I am wondering what was wrong with my trr file of B . I appreciate for any suggestions! Sincerely Xiaojia -- 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: cannot read frames out from trr files
Sorry for the typo, the last evidence4) I also compared the generated files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching 100ns, the size would **NOT*** be the same as A. On Wed, Apr 3, 2013 at 7:25 PM, mu xiaojia muxiaojia2...@gmail.com wrote: Dear GMX users, I am not sure if someone has similar problems before. I cannot read half of the frames from trr file after md simulation, and I believe my simulation has already completed. I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the only difference between A and B is they are npt simulations under different temperature (in mdp file, ref_t part )and such difference would not cause crash of the simulation. I have successfully finished A, everything looks perfect (frames can be successfully extracted), but for B, I could not extract last 70ns' frames from trr. 1) My command is like: mdrun_mpi -s -deffnm MD_A -cpi -append, because I am using super computer so the job will be restarted for multiple times. 2) both simulation are 100ns, both log files indicate that they have finished 100ns simulations. I checked my screen out put for B, whenever it restarted, the output on screen is correct and continuously ( something like: 1 steps, 10.0 ps (continuing from step 95963500, 95963.5 ps). 3) With gmxcheck, it looks that my B simulation only reached 29,7ns(which means only the first two restart simulation were recorded into trr, which log files are not saying in this way.) * * *For system A (the successful one), it shows* Reading frame 0 time0.000 # Atoms 72166 Last frame 2000 time 10.000 Item#frames Timestep (ps) Step 200150 Time 200150 Lambda 200150 Coords 200150 Velocities 200150 Forces 0 Box200150 *for system B (the failed one)* Reading frame 0 time0.000 # Atoms 72166 Reading frame 500 time 25000.000 Item#frames Timestep (ps) Step 59650 Time 59650 Lambda 59650 Coords 59650 Velocities 59650 Forces 0 Box59650 4) I also compared the generated files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching 100ns, the size would be the same as A. I am wondering what was wrong with my trr file of B . I appreciate for any suggestions! Sincerely Xiaojia -- 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: cannot read frames out from trr files
On 4/3/13 8:42 PM, mu xiaojia wrote: Sorry for the typo, the last evidence4) I also compared the generated files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching 100ns, the size would **NOT*** be the same as A. You probably have a corrupted frame. The simulation continued and the .trr file continued being written, so you see comparable file sizes. -Justin On Wed, Apr 3, 2013 at 7:25 PM, mu xiaojia muxiaojia2...@gmail.com wrote: Dear GMX users, I am not sure if someone has similar problems before. I cannot read half of the frames from trr file after md simulation, and I believe my simulation has already completed. I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the only difference between A and B is they are npt simulations under different temperature (in mdp file, ref_t part )and such difference would not cause crash of the simulation. I have successfully finished A, everything looks perfect (frames can be successfully extracted), but for B, I could not extract last 70ns' frames from trr. 1) My command is like: mdrun_mpi -s -deffnm MD_A -cpi -append, because I am using super computer so the job will be restarted for multiple times. 2) both simulation are 100ns, both log files indicate that they have finished 100ns simulations. I checked my screen out put for B, whenever it restarted, the output on screen is correct and continuously ( something like: 1 steps, 10.0 ps (continuing from step 95963500, 95963.5 ps). 3) With gmxcheck, it looks that my B simulation only reached 29,7ns(which means only the first two restart simulation were recorded into trr, which log files are not saying in this way.) * * *For system A (the successful one), it shows* Reading frame 0 time0.000 # Atoms 72166 Last frame 2000 time 10.000 Item#frames Timestep (ps) Step 200150 Time 200150 Lambda 200150 Coords 200150 Velocities 200150 Forces 0 Box200150 *for system B (the failed one)* Reading frame 0 time0.000 # Atoms 72166 Reading frame 500 time 25000.000 Item#frames Timestep (ps) Step 59650 Time 59650 Lambda 59650 Coords 59650 Velocities 59650 Forces 0 Box59650 4) I also compared the generated files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching 100ns, the size would be the same as A. I am wondering what was wrong with my trr file of B . I appreciate for any suggestions! Sincerely Xiaojia -- 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: Applying periodic boundary conditions in energy minimization
Hi, I have a polymer box on which I wish to apply energy minimization. However, when I do energy minimization runs to polymer chain unravels and goes out of the box. I guess this is because periodic conditions are not applied. My em.mdp file is: ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1000 ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1 rvdw= 1 Tcoupl = no Pcoupl = no gen_vel = no pbc = xyz This last line means PBC are being applied. Your observations are consistent with using a box that is too small for the solute, but since you haven't supplied information as to (1) what the system is, (2) how you built it, or (3) how large the box is, there's very little to say beyond speculation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin I am using a composite system of polymer and clay. The composite box (5.8 nm * 5.8 nm *7 nm) is made from combining a polymer box (5.7 nm * 5.7 nm * 5.7 nm) and clay box (5.5 nm * 5.1 nm * 1 nm) using editconf and genbox. Should I increase the size of the composite box. Also, If I increase the size of the box how do I ensure that the density of the system does not chance. Thanks for your help. -- 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] surface tension
Hello all, Does anyone know how one can study the effect of pressure on surface tension of pure liquids? Thanks, -- 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] Salt bridge observation
Sir, That is true, previously you had explained regarding this. Calculation using g_saltbr 1. For g_saltbr I included the following residues - ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated which contained only these residues. sb was calculated using - g_saltbr -f traj.xtc -s md.tpr -b 4000 -e 4000 -t 0.4 -sep 2. Files that were generated were filtered and only those having sb between ASP, GLU and ARG LYS were retained. 3. Further, out of these sbs, those which had the following atoms CG ASP, CD GLU, NE ARG, NH1 ARG, NH2 ARG, NZ LYS were retained. Calculation using g_hbond - It was done using the index file mentioned in my previous post using g_hbond -f traj.xtc -s md.tpr -n sb.ndx -contact -r 0.4 -hbm ghbond.xpm -hbn ghbond.ndx -num ghbond.xvg -b 4000 -e 4000 So essentially the final results in both are composed of sbs formed between ASP. GLU and ARG LYS. (charged groups in case of g_saltbr while charged atoms in case of g_hbond. The comparison showed that all sbs from g_hbond were present in the output from g_saltbr. But g_saltbr had some additional sbs off-course between the same charged groups. But only the distance was greater than 4 Ang for ex- distance between NH2 ARG and OD2 ASP is 4.32Ang Since it considers charged group CG of ASP instead of OD2 ASP distance between NH2 ARG and CG ASP is 5.54 Ang There are some 10 more such examples. I can send the calculations if requires. Thank you Regards Kavya On Wed, Apr 3, 2013 at 10:25 PM, Justin Lemkul jalem...@vt.edu wrote: On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, This is regarding an observation while calculating the salt bridge (sb) using g_saltbr. I used g_saltbr and g_hbond (with contact option) with a cut of of 4Ang, for calculating sb in the whole protein at a single frame. I made sure that I considered sb between same set of residues (ASP, GLU with LYS ARG) in both calculations. and filtered accordingly. While checking the individual sb it was found that most of the results from g_saltbr matches with g_hbond but g_saltbr gives some extra sbs. On checking these extra sb it was found that the distance between the atoms forming sb are more than the cut of I had mentioned (4 Ang). Not sure why it is like this. But just wanted to convey this observation. Please provide a concrete example. Note that running g_saltbr and g_hbond (with the index files mentioned before) should not be expected to produce equivalent result. g_saltbr is relatively stupid; it considers any group with a charge ± 0.2 to be capable of participating in a salt bridge. In some cases, this will include methylene groups or others than are near the actual charged groups. Such behavior could easily account for whatever observation you're making. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] Simulation of the HEM-containing proteins
It was strange for me the big number of such errors :) May the construction of new scheme for the hydrogens in the .hdb file partly solve my problem ? ( as I've mentioned previously i had mismatch in 2 hydrogens ( in comparison to the NMR-like structure). Should also HEME be added in the residuetype.dat as the part of the protein? Finally I'll be thankful to everyone who could provide me with the any cytochrome properly parametrized in charmm :) James 2013/4/3 Justin Lemkul jalem...@vt.edu On Wed, Apr 3, 2013 at 10:27 AM, James Starlight jmsstarli...@gmail.com wrote: I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but after processing that structure to grompp I've obtained errors like ERROR 1 [file topol.top, line 2106]: No default Bond types ERROR 2 [file topol.top, line 2144]: No default Bond types ERROR 3 [file topol.top, line 3153]: No default Bond types ERROR 4 [file topol.top, line 8725]: No default U-B types ERROR 5 [file topol.top, line 8792]: No default U-B types ERROR 6 [file topol.top, line 10624]: No default U-B types ERROR 7 [file topol.top, line 10625]: No default U-B types ERROR 8 [file topol.top, line 11382]: No default U-B types ERROR 9 [file topol.top, line 11383]: No default U-B types ERROR 10 [file topol.top, line 11384]: No default U-B types ERROR 11 [file topol.top, line 11385]: No default U-B types ERROR 12 [file topol.top, line 11491]: No default U-B types ERROR 13 [file topol.top, line 11492]: No default U-B types ERROR 14 [file topol.top, line 11493]: No default U-B types ERROR 15 [file topol.top, line 11506]: No default U-B types ERROR 16 [file topol.top, line 11507]: No default U-B types ERROR 17 [file topol.top, line 11508]: No default U-B types ERROR 18 [file topol.top, line 12147]: No default Proper Dih. types ERROR 19 [file topol.top, line 12148]: No default Proper Dih. types ERROR 20 [file topol.top, line 12149]: No default Proper Dih. types ERROR 21 [file topol.top, line 12150]: No default Proper Dih. types ERROR 22 [file topol.top, line 12151]: No default Proper Dih. types ERROR 23 [file topol.top, line 12152]: No default Proper Dih. types ERROR 24 [file topol.top, line 12247]: No default Proper Dih. types ERROR 25 [file topol.top, line 12248]: No default Proper Dih. types ERROR 26 [file topol.top, line 12249]: No default Proper Dih. types ERROR 27 [file topol.top, line 12250]: No default Proper Dih. types ERROR 28 [file topol.top, line 12251]: No default Proper Dih. types ERROR 29 [file topol.top, line 12252]: No default Proper Dih. types ERROR 30 [file topol.top, line 14948]: No default Proper Dih. types ERROR 31 [file topol.top, line 14950]: No default Proper Dih. types ERROR 32 [file topol.top, line 14952]: No default Proper Dih. types ERROR 33 [file topol.top, line 14956]: No default Proper Dih. types ERROR 34 [file topol.top, line 14957]: No default Proper Dih. types ERROR 35 [file topol.top, line 14958]: No default Proper Dih. types ERROR 36 [file topol.top, line 14959]: No default Proper Dih. types ERROR 37 [file topol.top, line 14960]: No default Proper Dih. types ERROR 38 [file topol.top, line 14961]: No default Proper Dih. types ERROR 39 [file topol.top, line 14962]: No default Proper Dih. types ERROR 40 [file topol.top, line 14963]: No default Proper Dih. types ERROR 41 [file topol.top, line 14964]: No default Proper Dih. types ERROR 42 [file topol.top, line 14965]: No default Proper Dih. types ERROR 43 [file topol.top, line 14966]: No default Proper Dih. types ERROR 44 [file topol.top, line 16263]: No default Proper Dih. types ERROR 45 [file topol.top, line 16264]: No default Proper Dih. types ERROR 46 [file topol.top, line 16269]: No default Proper Dih. types ERROR 47 [file topol.top, line 16270]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 3 [file topol.top, line 16745]: System has non-zero total charge: 7.01 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. --- Program grompp, VERSION 4.6 Source code file: /home/own/Documents/distr/gromacs-4.6/src/kernel/grompp.c, line: 1593 Fatal error: There were 47 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at
[gmx-users] installating GROMACS on windows 7 64 bit system
i followed the following steps to install gromacs : 1. Download cygwin from http://www.cygwin.com/ .Installed packages including gdb, make and tcsh NOTE : i was not able to find package gdn 2. Downloaded GROMACS (gromacs-4.0.7) source code. 3. Downloaded fftw-3.2.1.tar.gz 4. Extracted to C:\fftw-3.2.1 5. start cygwin and change the directory to your FFTW folder: cd c:\fftw-3.2.1 6. ./configure --enable-threads --enable-sse --enable-float 7. make 8. make install 9. make distclean 10. Extracted gromacs to C:\gromacs-4.0.7 and in the cygwin console, changed directory to the gromacs folder: cd C:\gromacs-4.0.7 11. ./configure --enable-shared LDFLAGS='-L/usr/local/lib' 12. make 13. make install 14. make links 15. make clean 16. i downloaded the test set gmxtest-4.0.4 and extracted it to C:\gmxtest 17. in the cygwin console, changed directory to the gmxtest folder: cd C:\gmxtest 18. source /usr/local/gromacs/bin/GMXRC 19. ./gmxtest.pl all Got the following result $ ./gmxtest.pl all All 16 simple tests PASSED FAILED. Check files in aminoacids FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in water 4 out of 14 complex tests FAILED FAILED. Check files in kernel020 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 16 out of 63 kernel tests FAILED N Reference This test 10-33.9883-29.5518 11-33.9883-29.5518 There were 2 differences in final energy with the reference file All 45 pdb2gmx tests PASSED pdb2gmx tests FAILED what is the error and how can i eliminate it ? -- View this message in context: http://gromacs.5086.n6.nabble.com/installating-GROMACS-on-windows-7-64-bit-system-tp5006901.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
