[gmx-users] confusion of forward and backward FEP in Gromacs-4.6.5
Hi all, I want to calculate the free energy difference for ATP--GTP in solution, for the forward analysis, the parameters for free energy perturbation are as follows: free-energy = yes sc-alpha = 0.3 sc-power = 1 sc-sigma = 0.25 sc-coul = no couple-intramol = yes init-lambda-state= $LAMBDA$ coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 nstdhdl = 50 calc-lambda-neighbors= 1 The calculated free energy difference is about -273 kJ/mol. In order to check the FEP convergence, backward analysis was also done. I adopt two ways to carry out backward analysis. (1) Modify the topology file for GTP-- ATP , the parameters of free energy calculation is the same as forward analysis. And the free energy difference of backward is about 213 kJ/mol. （2）Using the same topology file as forward analysis. But modify the parameter settings of coul-lambdas and vdw-lambdas for free energy calculation shown as follows free-energy = yes sc-alpha = 0.3 sc-power = 1 sc-sigma = 0.25 sc-coul = no couple-intramol = yes init-lambda-state= $LAMBDA$ coul-lambdas = 1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 vdw-lambdas = 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.95 0.9 0.85 0.8 0.75 0.7 0.65 0.6 0.55 0.5 0.45 0.4 0.35 0.3 0.25 0.2 0.15 0.1 0.05 0.0 nstdhdl = 50 calc-lambda-neighbors= 1 The calculated free energy difference is about 272 kJ/mol Theoretically, the two ways of backward analysis is the same. And the values of free energy should be identical. Now, I am confused whether I misunderstand something or set the wrong parameters for FEP calculation. Would you like to give me some help？ Thanks in advance. Best wishes Duan Baogen Beijing Computational Science Research Center -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] EnMin constraints: Hamletic doubt
Dear GMX community, I am running simulations of a solvated protein on a (frozen) Au substrate, but I think that my question is so basic that it falls outside the details of my case... So, the question is: when I prepare the system by minimizing the energy, should I set constraints = all_bonds, h_bonds or none? IMHP, I should set it to all_bonds, otherwise I may risk that the system's energy minimum corresponds to a configuration very different from the initial one... However, I saw somebody is using constraints = none and I was wandering why... Would somebody take the pleasure to embark on the discussion of such an issue with me? Thnx in advance, Nicola -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem in running protein-ligand (Heteroatom type) system: Ligand position not in correct position
Dear gromacs Users, I am running a simulation of Protein-Ligand complex. In this case, the ligand consists of a GTP molecule, whose parameters I am deriving from PRODRG server. When I try to generate the complex using coordinates obtained from PRODRG for GTP and from pdb2gmx for Protein, the position of ligand is not the same. I am following these steps in building this protein-ligand complex. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html I have followed the same set-up previously, for the same system and it worked fine then but now it is not. Can anyone help me out and let me know where I am wrong. Any suggestion would be welcome. Thanks. --Neeru Sharma, Centre for Development of Advanced Computing (CDAC), Pune, India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Hydrogen bond existence map
Hi all I would like to create hydrogen bond existence map for interaction of each residue with my ligand. I am aware that -hbm and -hbn option of g_hbond along with index file would serve the purpose. But the resulting output file is giving existence map for each atom of the residue. Instead, I want one map for residue as a whole. Example if any residue of protein is forming hydrogen bond with my ligand for certain time through bond A but for the remaining time it forms through bond B, then I want the map to show presence of hydrogen bond through one single line during the entire course of simulation. Is it possible with gromacs? Thanks in advance Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] More suitable force field and water model
Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose. As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. I think it is also related to properties of our system components (charge, etc.). for example for sugars or lipids. Is there any article which has compared these in details? Please let me know. any suggestion is appreciated in advance Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Hydrogen bond existence map
Hi Nidhi, Only with post processing of named files I'm afraid. Kind regards, Erik On 19 Jun 2014, at 10:48, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hi all I would like to create hydrogen bond existence map for interaction of each residue with my ligand. I am aware that -hbm and -hbn option of g_hbond along with index file would serve the purpose. But the resulting output file is giving existence map for each atom of the residue. Instead, I want one map for residue as a whole. Example if any residue of protein is forming hydrogen bond with my ligand for certain time through bond A but for the remaining time it forms through bond B, then I want the map to show presence of hydrogen bond through one single line during the entire course of simulation. Is it possible with gromacs? Thanks in advance Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx
Thank you very much for your quick reply, My peptide is only composed of amino acids, and it has a total charge of 0. My termini are NH2 and COOH (so the termini are not ionized). My force field is amber99sb. I tried to change for all atoms of my first residue (ASN) the ASN residue with the NASN residue name. In the first residue (ASN) there are the 3 atoms of N terminal . In the same way for ARG (the last residue ) with CARG. With -inter option in the pdb2gmx command, If I select Not protonated ARG (charge 0) and the other residues with charge 0, at the end the command says: Fatal error In the chosen force field there is no residue type for 'ARGN' as an ending terminus if I select protonated ARG (charge 1) and the other residues with charge 0, I obtain charge 1 (it is obvious) but my NH2 termini is changed to NH3 and my COOH in COO. (The command works but in my case the result is wrong because the total charge has to be 0 with NH2 and COOH termini, not ionized). I don't understand if in my case I have to change ASN to NASN only for the 3 atoms in N terminal( N,H,H) and to change ARG to CARG only for the 4 atoms in C terminal ( C,O2,O1,H) or change for all atoms of the first residue (ASN), ASN with NASN, and change all atoms of the last residue (ARG) , ARG with CARG.( that I done and described before).. If this is the right way, I don't know how to obtain the right result for my peptide. Could you help me? I attached my original .pdb file (not edited), and my edited pdb file. Thank you very much, Mirko On Wednesday, June 18, 2014 5:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/18/14, 11:18 AM, mirko busato wrote: Dear Users, I am using the command pdb2gmx_d on a neutral peptide in this way: pdb2gmx_d -f pep2_n.pdb -water none -inter My force field is AMBER. The first residue is ASN and the last residue is ARG My terminals are not ionized (NH2 and COOH). So I changed the name of residue ASN in NME for the 3 atoms (N,NH2,NH1), and I changed the name of residue LYS in ACE for the 4 atoms (C,O2,O1,H2). If in the interactive way I select ARG (not protonated) ,I obtained a message like that Fatal error: In the chosen force field there is no residue type for 'ARGN' . After I tried to select ARG(protonated) and I obtained this error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Fix your terminal residues so that they match the residue database (.rtp) entries, or provide terminal database entries (.tdb). Could you help me? If you have non-amino acids as the termini (i.e. capping groups), you need to select None for both termini. The side chain protonation is irrelevant to the treatment of the actual termini. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ==-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] EnMin constraints: Hamletic doubt
On 6/19/14, 4:11 AM, Nicola Staffolani wrote: Dear GMX community, I am running simulations of a solvated protein on a (frozen) Au substrate, but I think that my question is so basic that it falls outside the details of my case... So, the question is: when I prepare the system by minimizing the energy, should I set constraints = all_bonds, h_bonds or none? What was your force field parametrized to use? Most commonly, modern force fields constrain bonds involving H, though all bonds are frequently constrained in practice because the differences are generally small and the rigid representation of a bond is considered by many to be a more realistic representation of the ground state than a harmonic function. IMHP, I should set it to all_bonds, otherwise I may risk that the system's energy minimum corresponds to a configuration very different from the initial one... However, I saw somebody is using constraints = none and I was wandering why... Without context, answering that is impossible. Would somebody take the pleasure to embark on the discussion of such an issue with me? Thnx in advance, There have been numerous discussions on the underlying theory of constraints and their proper application; a bit of searching should turn them up. Several have occurred very recently on this very list. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] More suitable force field and water model
On 6/19/14, 5:59 AM, Mohsen Ramezanpour wrote: Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose. This is actually very straightforward. Every force field was parametrized using a certain water model. That's the one you use unless there is clear evidence that a different model works better for some reason. There are very few deviations from the original parametrizations of which I am aware, and most improvements are only small. As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Without context, there's not much value to that statement. On their own, some water models reproduce certain bulk properties better than others, but no water model is perfect. If you were to combine TIP4P with Gromos or something, I'd say that's probably unsound, even if TIP4P is better in terms of whatever you've chosen to look at. Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. That's not necessarily true; I've seen demonstrations of other combinations yielding very good hydration free energies. In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. If you're using Gromos96 53a6, it is known to produce helical instability. So the hydration free energies may be good, but the structure of the protein may suffer from artifacts. I think it is also related to properties of our system components (charge, etc.). for example for sugars or lipids. Is there any article which has compared these in details? Please let me know. dx.doi.org/10.1021/jp0641029 -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx
On 6/19/14, 8:59 AM, mirko busato wrote: Thank you very much for your quick reply, My peptide is only composed of amino acids, and it has a total charge of 0. My termini are NH2 and COOH (so the termini are not ionized). My force field is amber99sb. I tried to change for all atoms of my first residue (ASN) the ASN residue with the NASN residue name. In the first residue (ASN) there are the 3 atoms of N terminal . In the same way for ARG (the last residue ) with CARG. Look at the force field .rtp file - you will see that the Amber termini are predefined and they are always charged. That is an unfortunate limitation to the current implementation. I suspect someone must have produced neutral forms of the termini, but you'll have to add them yourself if you want to do such a simulation with this force field. With -inter option in the pdb2gmx command, If I select Not protonated ARG (charge 0) and the other residues with charge 0, at the end the command says: Fatal error In the chosen force field there is no residue type for 'ARGN' as an ending terminus This option chooses the side chain protonation state, not the terminus. if I select protonated ARG (charge 1) and the other residues with charge 0, I obtain charge 1 (it is obvious) but my NH2 termini is changed to NH3 and my COOH in COO. (The command works but in my case the result is wrong because the total charge has to be 0 with NH2 and COOH termini, not ionized). I don't understand if in my case I have to change ASN to NASN only for the 3 atoms in N terminal( N,H,H) and to change ARG to CARG only for the 4 atoms in C terminal ( C,O2,O1,H) or change for all atoms of the first residue (ASN), ASN with NASN, and change all atoms of the last residue (ARG) , ARG with CARG.( that I done and described before).. If this is the right way, I don't know how to obtain the right result for my peptide. As stated above, you'll have to modify the force field to add appropriate parameters or otherwise use a different force field that actually allows you to choose terminus protonation state. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Angle constraints independent on bond constraints
Dear all, I want to study vibrational dynamics and have an HDO molecule (D: Deuterium) in a bulk water surrounding as a test case. In a test calculation I want to fix the OD bond and the HOD angle whereas the OH bond shall be allowed to vibrate. Fixing the OD bond is no problem but the angle constraints seem to be more problematic. So far I have found in the manual and in previous posts that fixing the angle amounts to fixing the whole triangle via bond constraints which is not suitable for my purpose. Is there any chance to do angle constraints for a particular molecule independent on bond constraints? Greetings Fabian Gottwald -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] More suitable force field and water model
Dear Justin, On Thu, Jun 19, 2014 at 3:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/19/14, 5:59 AM, Mohsen Ramezanpour wrote: Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose. This is actually very straightforward. Every force field was parametrized using a certain water model. That's the one you use unless there is clear evidence that a different model works better for some reason. There are very few deviations from the original parametrizations of which I am aware, and most improvements are only small. As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Without context, there's not much value to that statement. On their own, some water models reproduce certain bulk properties better than others, but no water model is perfect. If you were to combine TIP4P with Gromos or something, I'd say that's probably unsound, even if TIP4P is better in terms of whatever you've chosen to look at. Yes, Please have a look at the abstract ( http://www.ncbi.nlm.nih.gov/pubmed/16178604) and also the conclusion of ( http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482) What do you mean exactly by something? do you mean TIP4P does not behave good enough in combination with other force fields too?! Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. That's not necessarily true; I've seen demonstrations of other combinations yielding very good hydration free energies. You are right, but some of them give more precise results and work for most cases! The conclusion of ( http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482) In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. If you're using Gromos96 53a6, it is known to produce helical instability. So the hydration free energies may be good, but the structure of the protein may suffer from artifacts. Yes, I want to use this ff because of our main quantities of interest. But we also are interested in other quantities (for example our active site structure which is composed of helices, its flexibility, etc). the main problem I mentioned was: How can we rely on other quantities from our simulation while we have chosen some special combinations? No body has investigated all quantities of simulation for all ff and water models combinations, what can be the solution? I think it is also related to properties of our system components (charge, etc.). for example for sugars or lipids. Is there any article which has compared these in details? Please let me know. dx.doi.org/10.1021/jp0641029 Some of my comments was from the same article! please have a look at the abstract and conclusion Thanks in advance -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] EnMin constraints: Hamletic doubt
Dear Justin, thank u 4 replying! On 19 June 2014 15:04, Justin Lemkul jalem...@vt.edu wrote: On 6/19/14, 4:11 AM, Nicola Staffolani wrote: Dear GMX community, I am running simulations of a solvated protein on a (frozen) Au substrate, but I think that my question is so basic that it falls outside the details of my case... So, the question is: when I prepare the system by minimizing the energy, should I set constraints = all_bonds, h_bonds or none? What was your force field parametrized to use? Most commonly, modern force fields constrain bonds involving H, though all bonds are frequently constrained in practice because the differences are generally small and the rigid representation of a bond is considered by many to be a more realistic representation of the ground state than a harmonic function. I do not understand your question... Do you mean which force field I am using? In this case the answer is gromos43a1... IMHP, I should set it to all_bonds, otherwise I may risk that the system's energy minimum corresponds to a configuration very different from the initial one... However, I saw somebody is using constraints = none and I was wandering why... Without context, answering that is impossible. I see... How can I better describe the context ? Which info do u need? I have seen setting the constraints to none with the same very system as mines (solvated azurin on Au layers) where the ff used was again gromos43a1... Would somebody take the pleasure to embark on the discussion of such an issue with me? Thnx in advance, There ha ve been numerous discussions on the underlying theory of constraints and their proper application; a bit of searching should turn them up. Several have occurred very recently on this very list. -Justin Thank you very much again for answering! Regards, Nicola -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- New ideas, fragile as spring flowers, easily bruised by the tread of the multitude, may yet be cherished by the solitary wanderer., Fred Hoyle, *The Black Cloud*. Everybody knows that something can't be done until somebody turns up who doesn't know that it can't be done and he does it., Albert Einstein Sometime ago I met a fellow who was wearing an abnormally long tie - I mean, it was abnormally long because of how the knot had been made, not because the tie was an abnormally long one, and so I asked him why such an abnormally long tie, and you know what he told me? That the tie belonged to his grandfather!! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] maximum number of specbonds?
Hi, I am parameterizing an artifical ligand. I use small residue-like fragments and connect them with specbonds in a grid, since I need arbitrary shapes and sizes. Now, I ran into segmentation faults, when the grid becomes to large. Is there an upper limit for the specbonds? How can I fix that or do you see a better way to solve that issue? Thanks Soren -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] maximum number of specbonds?
Something is really weird about that system. The error message changes with the number of residues I use. Everything works fine for 2 and 3 residues. With 4 residues I get : ___ Warning: Starting residue DUL1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue DUL2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue DUL3 in chain not identified as Protein/RNA/DNA. Warning: Starting residue DUL4 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 11 out of 11 lines of specbond.dat converted successfully Special Atom Distance matrix: DUL1DUL1DUL1DUL2DUL2DUL2DUL3 DU01DU12DU23DU04DU15DU26DU07 DUL1DU12 0.200 DUL1DU23 0.346 0.200 DUL2DU04 0.400 0.346 0.529 DUL2DU15 0.529 0.400 0.529 0.200 DUL2DU26 0.529 0.346 0.400 0.346 0.200 DUL3DU07 0.400 0.600 0.721 0.693 0.872 0.916 DUL3DU18 0.200 0.400 0.529 0.529 0.693 0.721 0.200 DUL3DU29 0.200 0.346 0.400 0.600 0.721 0.693 0.346 DUL4 DU010 0.400 0.529 0.721 0.400 0.600 0.721 0.400 DUL4 DU111 0.346 0.400 0.600 0.200 0.400 0.529 0.529 DUL4 DU212 0.200 0.200 0.400 0.200 0.346 0.400 0.529 DUL3DUL3DUL4DUL4 DU18DU29 DU010 DU111 DUL3DU29 0.200 DUL4 DU010 0.346 0.529 DUL4 DU111 0.400 0.529 0.200 DUL4 DU212 0.346 0.400 0.346 0.200 Linking DUL-1 DU0-1 and DUL-1 DU1-2... Linking DUL-1 DU0-1 and DUL-3 DU1-8... Linking DUL-1 DU0-1 and DUL-3 DU2-9... Linking DUL-1 DU0-1 and DUL-4 DU2-12... Linking DUL-1 DU1-2 and DUL-1 DU2-3... Linking DUL-1 DU1-2 and DUL-4 DU2-12... Linking DUL-2 DU0-4 and DUL-2 DU1-5... Linking DUL-2 DU0-4 and DUL-4 DU1-11... Linking DUL-2 DU0-4 and DUL-4 DU2-12... Linking DUL-2 DU1-5 and DUL-2 DU2-6... Linking DUL-3 DU0-7 and DUL-3 DU1-8... Linking DUL-3 DU1-8 and DUL-3 DU2-9... Linking DUL-4 DU0-10 and DUL-4 DU1-11... Linking DUL-4 DU1-11 and DUL-4 DU2-12... Segmentation fault (core dumped) ___ and with 5 residues: ___ inking DUL-1 DU0-1 and DUL-1 DU1-2... Linking DUL-1 DU0-1 and DUL-3 DU1-8... Linking DUL-1 DU0-1 and DUL-3 DU2-9... Linking DUL-1 DU0-1 and DUL-4 DU2-12... Linking DUL-1 DU1-2 and DUL-1 DU2-3... Linking DUL-1 DU1-2 and DUL-4 DU2-12... Linking DUL-2 DU0-4 and DUL-2 DU1-5... Linking DUL-2 DU0-4 and DUL-4 DU1-11... Linking DUL-2 DU0-4 and DUL-4 DU2-12... Linking DUL-2 DU0-4 and DUL-5 DU2-15... Linking DUL-2 DU1-5 and DUL-2 DU2-6... Linking DUL-2 DU1-5 and DUL-5 DU2-15... Linking DUL-3 DU0-7 and DUL-3 DU1-8... Linking DUL-3 DU1-8 and DUL-3 DU2-9... Linking DUL-4 DU0-10 and DUL-4 DU1-11... Linking DUL-4 DU1-11 and DUL-4 DU2-12... Linking DUL-5 DU0-13 and DUL-5 DU1-14... Linking DUL-5 DU1-14 and DUL-5 DU2-15... Opening force field file /home/swacker/System/gromacs/GMX46/amber99sb-ildn.ff/aminoacids.arn Opening force field file /home/swacker/System/gromacs/GMX46/amber99sb-ildn.ff/dna.arn Opening force field file /home/swacker/System/gromacs/GMX46/amber99sb-ildn.ff/rna.arn Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 5 residues with 15 atoms Making bonds... --- Program gmx pdb2gmx, VERSION 5.1-dev-20140607-3db1d85 Source code file: /home/swacker/Install_Software/gromacs/src/gromacs/gmxpreprocess/pgutil.c, line: 125 Fatal error: Residue 1 named DUL of a molecule in the input file was mapped to an entry in the topology database, but the atom used in an interaction of type special bond in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. ___ my specbonds.dat: ___ 11 CYS SG 1 CYS SG 1 0.2 CYS2CYS2 CYS SG 1 HEM FE 2 0.25CYS2HEME CYS SG 1 HEM CAB 1 0.18CYS2HEME CYS SG 1 HEM CAC 1 0.18CYS2HEME HIS NE2 1 HEM FE 1 0.2 HIS1HEME MET SD 1 HEM FE 1 0.24MET HEME CO C 1 HEMEFE 1 0.19CO HEME CYM SG 1 CYM SG 1 0.2 CYS2CYS2 DUL DU0 4 DUL DU1 4 0.2 DUL DUL DUL DU0 4 DUL DU2 4 0.2 DUL DUL DUL DU1 4 DUL DU2 4 0.2 DUL DUL ___ example.pdb
Re: [gmx-users] maximum number of specbonds?
Hi, It sounds like your practical options are to build some larger fragments to use when required, or generate your topology with something else, e.g. a custom script. pdb2gmx was built with slightly-branched polymers in mind, not much else. Mark On Thu, Jun 19, 2014 at 6:11 PM, Soren Wacker swac...@ucalgary.ca wrote: Hi, I am parameterizing an artifical ligand. I use small residue-like fragments and connect them with specbonds in a grid, since I need arbitrary shapes and sizes. Now, I ran into segmentation faults, when the grid becomes to large. Is there an upper limit for the specbonds? How can I fix that or do you see a better way to solve that issue? Thanks Soren -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
Ah, because it's Amber. Amber force fields are special and have specific nomenclature that signifies N- and C-termini, so they automatically get built. Changing the residue names by removing the N and C prefixes should fix things. Okay, which file do I remove the N and C prefixes from? Coordinate file, always manipulate the coordinate file. But the fact that you're asking this tells me that likely you never actually added those prefixes, so pdb2gmx is being smart and adding them for you. In that case, there's nothing you can do short of (1) modifying the pdb2gmx code, (2) manually hacking the topology - ugly, but effective, or (3) using a different force field that doesn't have terminus-specific naming (anything that's not Amber). After discussing it with my professor, he believes that I can attempt both (2) and (3) until one of them works. Currently, he and I are going through the process of designing a script to perform (2). Additionally, he told me that the only forcefields other than amber99sb that I can try are charmm27 and opls-aa. However, when I attempted to use either of those forcefields (these times I was relieved to finally see the option to select none for the termini), I received this error message: --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2top.c, line: 1109 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Does this have to do with the fact that I did select none for both terminals both of the times? Matthew -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] More suitable force field and water model
Hi, It would be miraculous if there was a good solution for all observables. A rigid, symmetric 3-point water molecule without VDW parameters on the the hydrogen atoms has 2 spatial, 2 charge, and 2 VDW parameters. That's not much freedom, and most of the 6-parameter space is obviously wrong, too. All you can do is pick a model that does something right (e.g. was the one used to parameterize the force field), accept that your model physics is a model, and remain alert for known and new problems. Even the quantum chemists argue about how to model small clusters of water! ;-) Mark On Thu, Jun 19, 2014 at 3:55 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Justin, On Thu, Jun 19, 2014 at 3:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/19/14, 5:59 AM, Mohsen Ramezanpour wrote: Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose. This is actually very straightforward. Every force field was parametrized using a certain water model. That's the one you use unless there is clear evidence that a different model works better for some reason. There are very few deviations from the original parametrizations of which I am aware, and most improvements are only small. As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Without context, there's not much value to that statement. On their own, some water models reproduce certain bulk properties better than others, but no water model is perfect. If you were to combine TIP4P with Gromos or something, I'd say that's probably unsound, even if TIP4P is better in terms of whatever you've chosen to look at. Yes, Please have a look at the abstract ( http://www.ncbi.nlm.nih.gov/pubmed/16178604) and also the conclusion of ( http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482) What do you mean exactly by something? do you mean TIP4P does not behave good enough in combination with other force fields too?! Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. That's not necessarily true; I've seen demonstrations of other combinations yielding very good hydration free energies. You are right, but some of them give more precise results and work for most cases! The conclusion of ( http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482) In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. If you're using Gromos96 53a6, it is known to produce helical instability. So the hydration free energies may be good, but the structure of the protein may suffer from artifacts. Yes, I want to use this ff because of our main quantities of interest. But we also are interested in other quantities (for example our active site structure which is composed of helices, its flexibility, etc). the main problem I mentioned was: How can we rely on other quantities from our simulation while we have chosen some special combinations? No body has investigated all quantities of simulation for all ff and water models combinations, what can be the solution? I think it is also related to properties of our system components (charge, etc.). for example for sugars or lipids. Is there any article which has compared these in details? Please let me know. dx.doi.org/10.1021/jp0641029 Some of my comments was from the same article! please have a look at the abstract and conclusion Thanks in advance -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441
Re: [gmx-users] Using specbond.dat in pdb2gmx
(Ignore the earlier message) Ah, because it's Amber. Amber force fields are special and have specific nomenclature that signifies N- and C-termini, so they automatically get built. Changing the residue names by removing the N and C prefixes should fix things. Okay, which file do I remove the N and C prefixes from? Coordinate file, always manipulate the coordinate file. But the fact that you're asking this tells me that likely you never actually added those prefixes, so pdb2gmx is being smart and adding them for you. In that case, there's nothing you can do short of (1) modifying the pdb2gmx code, (2) manually hacking the topology - ugly, but effective, or (3) using a different force field that doesn't have terminus-specific naming (anything that's not Amber). After discussing it with my professor, he believes that I can attempt both (2) and (3) until one of them works. Currently, he and I are going through the process of designing a script to perform (2). Additionally, he told me that the only forcefields other than amber99sb that I can try are charmm27 and opls-aa. However, when I attempted to use either of those forcefields (these times I was relieved to finally see the option to select none for the termini), I received this error message: --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2top.c, line: 1109 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Does this have to do with the fact that I did select none for both terminals both of the times? Here is the full command line: pdb2gmx_mpi -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter And because I do not want to leave any information out, here is the full text for each of these (the difference between the two forcefields being the selection of the respective forcefields): __ :-) pdb2gmx_mpi (-: Option Filename Type Description -f 1NB1.pdb InputStructure file: gro g96 pdb tpr etc. -o conf.gro Output Structure file: gro g96 pdb etc. -p topol.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsepenum id_or_ter Condition in PDB files when a new chain should be started (adding termini): id_or_ter, id_and_ter, ter, id or interactive -merge enum no Merge multiple chains into a single [moleculetype]: no, all or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum tip3p Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool yes Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool yes Interactive termini selection, instead of charged (default) -[no]lys bool no Interactive lysine selection, instead of charged -[no]arg bool no Interactive arginine selection, instead of charged -[no]asp bool no Interactive aspartic acid selection, instead of charged -[no]glu bool no Interactive glutamic acid selection, instead of charged -[no]gln bool no Interactive glutamine selection, instead of neutral -[no]his bool no Interactive histidine selection, instead of checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the coordinate file
[gmx-users] Velocities from checkpoint
Hello, I am running 30ns simulation divided into 30 1ns simulations. I am saving the velocities each 5fs and I can't run a single 30ns simulation with saving velocities each 5 fs. I am running 30 simulations,each is 1ns. I get the velocities and delete the trajectory and go for next simulation. for (( i = 1; i = 29; i++)) do grompp -f md.mdp -c structure_1.pdb -p structure_1.top -o structure_1.tpr mdrun -s structure_1.tpr -o structure_1.trr -c structure_1.pdb -e structure_1.edr -g structure_1.log rm -f *#* trjconv -f structure_1.trr -s structure_1.tpr -pbc nojump -o structure_1.gro EOF 0 EOF ./dipole_rotational_translational_moment_append.out rm -f *#* rm structure_1.gro rm structure_1.trr done Each simulation Gromacs generate the velocities randomly which are independent on previous simulation. Could it possible to get the velocities based on previous simulation. Thanks, Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] .rtp files
Dear Gromacs users; I use Gromacs version 4.5.4. I finished protein-ligand complex tutorial(Dr.justin lemkul tutorial). Now i want to use my ligand. I am new in this field(charge group blocking). For getting an idea about charge group blocking, i check .rtp files. cheking aminoacides.rtp files of gromos force field , it has ATP charge group blocking, but i didn't understand it and also i didn't find many of molecules ex. : TEMP, BA, RTOL, ... It would be greatly appreciated if anyone can help me in this field? Regards, N.P -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] EnMin constraints: Hamletic doubt
On 6/19/14, 10:05 AM, Nicola Staffolani wrote: Dear Justin, thank u 4 replying! On 19 June 2014 15:04, Justin Lemkul jalem...@vt.edu wrote: On 6/19/14, 4:11 AM, Nicola Staffolani wrote: Dear GMX community, I am running simulations of a solvated protein on a (frozen) Au substrate, but I think that my question is so basic that it falls outside the details of my case... So, the question is: when I prepare the system by minimizing the energy, should I set constraints = all_bonds, h_bonds or none? What was your force field parametrized to use? Most commonly, modern force fields constrain bonds involving H, though all bonds are frequently constrained in practice because the differences are generally small and the rigid representation of a bond is considered by many to be a more realistic representation of the ground state than a harmonic function. I do not understand your question... Do you mean which force field I am using? In this case the answer is gromos43a1... Constraining all bonds is common with Gromos96 parameter sets. I know that 53a6 was parametrized with all bonds constrained; I am not sure if the full details of 43a1 were ever published. If someone else knows, please chime in. The oldest public reference I know of for Gromos96 is a paper about the software suite in general, but not the original parametrization protocol. IMHP, I should set it to all_bonds, otherwise I may risk that the system's energy minimum corresponds to a configuration very different from the initial one... However, I saw somebody is using constraints = none and I was wandering why... Without context, answering that is impossible. I see... How can I better describe the context ? Which info do u need? I have seen setting the constraints to none with the same very system as mines (solvated azurin on Au layers) where the ff used was again gromos43a1... The context to which I refer is: what were the goals of the study? If one wants to examine, for instance, vibrational spectra, it would be inappropriate to apply constraints (and you'd be forced to use a very small time step). For normal MD investigations, constraints are used to increase the time step for better throughput. My comment about context is also a general one. People often mention previous posts without providing links or looking at the whole thread. There may be very specific reasons for a particular approach, or it may turn out that the posted settings were wrong ;) -Justin Would somebody take the pleasure to embark on the discussion of such an issue with me? Thnx in advance, There ha ve been numerous discussions on the underlying theory of constraints and their proper application; a bit of searching should turn them up. Several have occurred very recently on this very list. -Justin Thank you very much again for answering! Regards, Nicola -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Velocities from checkpoint
On 6/19/14, 4:12 PM, Nilesh Dhumal wrote: Hello, I am running 30ns simulation divided into 30 1ns simulations. I am saving the velocities each 5fs and I can't run a single 30ns simulation with saving velocities each 5 fs. I am running 30 simulations,each is 1ns. I get the velocities and delete the trajectory and go for next simulation. for (( i = 1; i = 29; i++)) do grompp -f md.mdp -c structure_1.pdb -p structure_1.top -o structure_1.tpr mdrun -s structure_1.tpr -o structure_1.trr -c structure_1.pdb -e structure_1.edr -g structure_1.log rm -f *#* trjconv -f structure_1.trr -s structure_1.tpr -pbc nojump -o structure_1.gro EOF 0 EOF ./dipole_rotational_translational_moment_append.out rm -f *#* rm structure_1.gro rm structure_1.trr done Each simulation Gromacs generate the velocities randomly which are independent on previous simulation. Could it possible to get the velocities based on previous simulation. You need to pass your .cpt file from the previous run to grompp -t. As it stands now, there is no relationship between the different segments of the run, and based on the fact that you're saying you get random velocities, your .mdp file probably has gen_vel = yes in it. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] .rtp files
On 6/19/14, 4:58 PM, Negar Parvizi wrote: Dear Gromacs users; I use Gromacs version 4.5.4. I finished protein-ligand complex tutorial(Dr.justin lemkul tutorial). Now i want to use my ligand. I am new in this field(charge group blocking). For getting an idea about charge group blocking, i check .rtp files. cheking aminoacides.rtp files of gromos force field , it has ATP charge group blocking, but i didn't understand it and also i didn't find many of molecules ex. : TEMP, BA, RTOL, ... It would be greatly appreciated if anyone can help me in this field? You need to tell us what ligand you're dealing with. A few other things to consider: 1. The manual has a very good description of what charge groups are and how they're designed. 2. If you're using PME, charge groups summing to zero or an integer is not strictly necessary. 3. If you're going to use the Verlet cutoff scheme for the simulation, charge groups are totally irrelevant. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/19/14, 3:00 PM, Matthew Stancea wrote: (Ignore the earlier message) Ah, because it's Amber. Amber force fields are special and have specific nomenclature that signifies N- and C-termini, so they automatically get built. Changing the residue names by removing the N and C prefixes should fix things. Okay, which file do I remove the N and C prefixes from? Coordinate file, always manipulate the coordinate file. But the fact that you're asking this tells me that likely you never actually added those prefixes, so pdb2gmx is being smart and adding them for you. In that case, there's nothing you can do short of (1) modifying the pdb2gmx code, (2) manually hacking the topology - ugly, but effective, or (3) using a different force field that doesn't have terminus-specific naming (anything that's not Amber). After discussing it with my professor, he believes that I can attempt both (2) and (3) until one of them works. Currently, he and I are going through the process of designing a script to perform (2). Additionally, he told me that the only forcefields other than amber99sb that I can try are charmm27 and opls-aa. However, when I attempted to use either of those forcefields (these times I was relieved to finally see the option to select none for the termini), I received this error message: --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2top.c, line: 1109 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Does this have to do with the fact that I did select none for both terminals both of the times? Yes, because pdb2gmx has difficulty figuring out that your termini have full valences on each of the atoms in the peptide bond. Special bonds and .rtp bonds are handled separately. If your input structure has all of the necessary hydrogen atoms (named correctly), then you *might* be able to get away with using the -missing flag. This is not something that is normally recommended, and it is potentially dangerous. Any topology generated with -missing should be scrutinized heavily to make sure everything is right. I can only think of one other constructive use of -missing, so be advised (and this goes for anyone else who comes across this post) that this is generally a very bad idea, so don't try to apply it in any other case. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
