Re: [gmx-users] Umbrella sampling for protein-drug system
Aldo Segura wrote: Dear gmx-users, I have following the umbrella sampling tutorial at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html. I’m trying to use it for a drug-protein system. In the tutorial the group A moves away to group B. I would like to pull the drug to the protein binding-site (i.e., drug move closer to protein). How can I do that? Should I modified the md_pull.mdp file (from the tutorial) changing the value from pull_rate1 (0.01) to a negative value (i.e. -0.01)? or using pull_geometry = position and related code instead pull_geometry = distance? You may have to make several changes. Changing the sign of pull_rate1 will indeed decrease the COM distance rather than increase it. Most of the pull_geometry values could be useful here, but changing the method may require other changes to the pulling settings. Refer to the manual. Note that hitting a moving target is substantially harder than inducing a simple dissociation of a protein complex, as the tutorial does. You may be able to carefully set a pull_group0 and an appropriate vector along which to pull your ligand, but if the protein diffuses or rotates even a small amount (which it will), you will likely crash your ligand into some non-target region. A variety of restraints could be used to prevent this from happening, but you may have a hard time ensuring that the restraints do not adversely affect the dynamics of the binding process. Probably a more effective approach is to start from a docked complex and pull the ligand out. If you're only looking for a PMF, you can accomplish the same results by doing so, and it is substantially easier. -Justin Thanks in advance, *//* */=== Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx mailto:asegu...@ipn.mx; aldoseg...@gmail.com mailto:aldoseg...@gmail.com =/* -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] configure: error: cannot compute sizeof (off_t)
Dear experts, I am still unable to overcome this error during the configuration: configure: error: cannot compute sizeof (off_t) See `config.log' for more details. I came across this thread with the exact same setup as I have: http://lists.gromacs.org/pipermail/gmx-users/2011-February/058369.html I have tried uninstalling openmpi 1.4.4 and installing the more stable openmpi1.4.3 but I am still experiencing the same error. ./configure --enable-mpi --program-suffix=_mpi MPICC=/usr/local/bin/mpicc --with-fft=fftw3 I have also tried to explicitly provide the path to mpicc as above but it still gives me the same error. This may or may not be relevant but at the end of the config.log there is also this line: configure: exit 77 Does that mean anything? Any help at all is appreciated! Thanks, 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] on force fields
Thanks for the reply on my first querry. I have another one. If I add a NEW atom type in *.atp file, will Gromacs automatically recognize this atom type? Thanks. --- On Wed, 2/16/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] on force fields To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, February 16, 2011, 1:53 PM On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote: Hi everyone! I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010). 1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to update if I need to switch to a new force field? You should make a copy of the whole force field directory into your working directory, rename the new directory suitably, make a suitable change to forcefield.doc, and then edit .itp files suitably. This means you're leaving your reference version untouched and can edit locally to your heart's content, and can be sure you're selecting the right force field with pdb2gmx and/or in your .top file. 2. The new force field 53ACARBO has a new gromos functional form for select torsional potentials. How to I go over implementing this in gromos? Preferably as a sum of existing functional forms. Or use tabulated bonded interactions (see manual and wiki). Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. 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] on force fields
Mr Bernard Ramos wrote: Thanks for the reply on my first querry. I have another one. If I add a NEW atom type in *.atp file, will Gromacs automatically recognize this atom type? Theoretically, yes, provided that you supply any corresponding parameters in, e.g., ffnonbonded.itp and ffbonded.itp. However, there is an unresolved bug related to atomtype assignment that may be relevant: http://redmine.gromacs.org/issues/618 It seems to me that any alterations to the .atp file cause things to break down, so do not be surprised if there are problems. -Justin Thanks. --- On *Wed, 2/16/11, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] on force fields To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, February 16, 2011, 1:53 PM On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote: Hi everyone! I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010). 1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to update if I need to switch to a new force field? You should make a copy of the whole force field directory into your working directory, rename the new directory suitably, make a suitable change to forcefield.doc, and then edit .itp files suitably. This means you're leaving your reference version untouched and can edit locally to your heart's content, and can be sure you're selecting the right force field with pdb2gmx and/or in your .top file. 2. The new force field 53ACARBO has a new gromos functional form for select torsional potentials. How to I go over implementing this in gromos? Preferably as a sum of existing functional forms. Or use tabulated bonded interactions (see manual and wiki). Mark -Inline Attachment Follows- -- gmx-users mailing listgmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] on force fields
Thank you, sir. That's nice of Gromacs to automatically assign new atom types from an input pdb file. I check out the link as well. --- On Mon, 2/21/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] on force fields To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, February 21, 2011, 10:41 AM Mr Bernard Ramos wrote: Thanks for the reply on my first querry. I have another one. If I add a NEW atom type in *.atp file, will Gromacs automatically recognize this atom type? Theoretically, yes, provided that you supply any corresponding parameters in, e.g., ffnonbonded.itp and ffbonded.itp. However, there is an unresolved bug related to atomtype assignment that may be relevant: http://redmine.gromacs.org/issues/618 It seems to me that any alterations to the .atp file cause things to break down, so do not be surprised if there are problems. -Justin Thanks. --- On *Wed, 2/16/11, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] on force fields To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, February 16, 2011, 1:53 PM On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote: Hi everyone! I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010). 1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to update if I need to switch to a new force field? You should make a copy of the whole force field directory into your working directory, rename the new directory suitably, make a suitable change to forcefield.doc, and then edit .itp files suitably. This means you're leaving your reference version untouched and can edit locally to your heart's content, and can be sure you're selecting the right force field with pdb2gmx and/or in your .top file. 2. The new force field 53ACARBO has a new gromos functional form for select torsional potentials. How to I go over implementing this in gromos? Preferably as a sum of existing functional forms. Or use tabulated bonded interactions (see manual and wiki). Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. 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] g_covar to calculate correlation of motion
Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using g_covar(the one which is available under http://www.gromacs.org/Downloads/User_contributions/Other_software) but it is not compatible with the GROMACS-4.5.3, so please suggest me the alternative way or does anyone have the modified g_covar for GROMKACS-4.5.3. -- * - Thanks and regards Bipin Singh * * * -- 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] about -CN triple bond
Hi, I added these words in the end of the topolgy [ virtual_sites2 ] ; Site from funct a 5 1 2 1 0.7439756 and changed the mass of the atom 5 to zero. When I performed the grompp before the MDS, it showed some error msg. Reading position restraint coords from em.gro Cleaning up constraints and constant bonded interactions with virtual sites ERROR: Cannot have constraint (5-7) with virtual site (5) ERROR: Cannot have constraint (5-6) with virtual site (5) ERROR: Cannot have constraint (4-5) with virtual site (5) --- Program grompp, VERSION 4.0.5 Source code file: vsite_parm.c, line: 856 Fatal error: There were 3 virtual sites involved in constraints --- I seems to need to exclude these atoms which link to the virtual atom. What should I deal with the problem? Thanks for your help. Best, Chia-yun 2011/2/19 Mark Abraham mark.abra...@anu.edu.au On 19/02/2011 5:18 PM, C.Y. Chang wrote: Hi, The errpr msg. that I expressed in the previous mail is unclear. It really happened in the grompp step of my dealinw with the em. The manual shows that the viste can be used by [ virtual sites2 ] That's misspelled too. Underscores are significant. You have to be literal when dealing with computers. ; Site from funct a 5 1 2 1 0.7439756 What should I choose the vsite for the -CN group? (2, 3fd or others?) The problems come when the force from normal angle and dihedral functions aren't numerically stable when there are 3 collinear atoms. The way to avoid this is to have one of those atoms virtual. Forces on it get projected onto the real atoms from which it is defined, the integration of forces proceeds only on the real atoms, and the position of the virtual site gets reconstructed later. So, which type do you think will work best here? I read the manual and the columns of the vsite need some parameters. The Site seems to be the atom number. Yes. The from seems some atom group, but which atoms should be included? The real atoms that form the virtual site. The number and order depends on the type of virtual site. Which atom is which is covered back in 4.7 You need to read that together with 5.2.2, like I said several emails ago. How could obtain the func values? That's situation-dependent. Here, you want to pick a position along the line that will lead to the three atoms being a sensible distance apart. Could you give me a molecule for my example? No, I don't have one. Your example above will construct atom 5 from 1 and 2 75% of the way along the line from 1 to 2, per Figure 4.16 and equation 4.134. Mark Thanks for your help. Best, Chia-yun 2011/2/19 Mark Abraham mark.abra...@anu.edu.au On 19/02/2011 3:02 PM, C.Y. Chang wrote: Hi, I have tried to add [ position restraints ] This is misspelled. Surely grompp warned about this? 2 1 1000 1000 1000 ; Restrain to a point 1 1 1000 0 1000 ; Restrain to a line (Y-axis) 3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane) in the end of the topology file. This does not even approach the solution to your problem. Position restraints inhibit diffusion and structural changes. You need a vsite, like you knew earlier. In the em. process, I get the eroor msg. No, this error happened in grompp. Fatal error: Invalid dihedral type 1000 GROMACS didn't recognise the mis-spelled directive, and so it's trying to make sense of your position restraint lines as dihedrals. Mark Chia-yun 2011/2/18 Mark Abraham mark.abra...@anu.edu.au On 18/02/2011 1:13 PM, C.Y. Chang wrote: Hi, I am dealing with the lipid bilayer permeation simulation. Most compounds can be finished, but the compounds with CN can't be performed simulation. I have searched the discussion in the gmx-users discussion. The vsite has been mentioned, and I have refered to the gromacs manual. But I don't understand that how I can use the vsite. The theory is discussed in chapter 4 and there's a brief example in 5.2.2. What have you tried and what went wrong? Mark (add the toplogy file or use the command line?) I attach the PDB and toplogy file of the molecule. First, I performed the molecular dynamic simulation for the pure lipid bilayer, and the step was been finished. After I insert the molecule, these command lines are performed. grompp -f minim.mdp -c cmplx.pdb -p topol_dppc.top -o em.tpr mdrun -v -deffnm em grompp -f npt_cmplx.mdp -c em.gro -p topol_dppc.top -o npt_cmplx.tpr nohup mdrun -v -deffnm npt_cmplx Thanks for your help. Best, Chia-yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] g_covar to calculate correlation of motion
Hi Bipin, Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific. Cheers, Tsjerk On Feb 21, 2011 8:05 AM, bipin singh bipinel...@gmail.com wrote: Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using g_covar(the one which is available under http://www.gromacs.org/Downloads/User_contributions/Other_software) but it is not compatible with the GROMACS-4.5.3, so please suggest me the alternative way or does anyone have the modified g_covar for GROMKACS-4.5.3. -- * - Thanks and regards Bipin Singh * * * -- 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] removing pbc jumps from trajectory
Hi I have a series of trajectories from a coarse grained simulation (Martini force field) that I ran using gromacs 4.0.4. The system consists of a protein embedded in a POPC bilayer solvated with water. During the simulation the protein (most of time its actually *part* of the protein) jumps across the pb into the neighboring box. I use a series of tcl scripts to analyse my trajectories and for that purpose I need to remove that period boundary jump and make the protein whole again. I have tried the approach described on the gromacs website http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions I also other combinations of -whole, -center and -pbc nojump of trjconv, without any luck. Can anyone suggest how I can re-center the protein and remove the pb jump ie make the protein whole Thanks Evelyne -- Evelyne Deplazes PhD student Theoretical Chemistry group University of Western Australia -- 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
