[gmx-users] [Fwd: installing gromacs on vista]
Hi, I am not a free private help service. Please search the GROMACS webpage first, where your question is answered. If you have a specific problem, please ask the mailing list. On point, GROMACS is a simulation package, not a molecule viewer. Mark Original Message Subject:installing gromacs on vista Date: Thu, 17 Dec 2009 00:59:12 -0800 (PST) From: maryam zargarzadeh maryamuni...@yahoo.com To: mark.abra...@anu.edu.au Dear Mark, I just need to open some molecule drawings with gromacs but I only have access to computer with vista. I looked at the website but it seems I can install gromacs on linuxs systems only. Is that the case or can you please help me with this? Is there any guideline on how to istall it on vista if possible. Thanks Regards, Maryam U of Alberta -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] How can I reconstruct the system in CGMD simulation?
greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? I have to switch back to the smaller radius afterward, Is it correct? if yes, How can I do it? I tried with editconf but could not. Best regards, Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
rasoul nasiri wrote: greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? Read up on your forcefield and find out how large the particles tend to be. It only has to be good enough, not perfect. I have to switch back to the smaller radius afterward, Is it correct? Changing what for what purpose? if yes, How can I do it? I tried with editconf but could not. I don't know what you mean. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are beads of protein from water beads with suitable van der wall distance (larger than 0.105nm), when I want to start production phase, first switch back to the smaller radius of van der waals of the water beads, then I will continue CGMD simulation. Is it possible I reduce this radius? Which commands of Gromacs suit can do it? Rasoul On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: rasoul nasiri wrote: greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? Read up on your forcefield and find out how large the particles tend to be. It only has to be good enough, not perfect. I have to switch back to the smaller radius afterward, Is it correct? Changing what for what purpose? if yes, How can I do it? I tried with editconf but could not. I don't know what you mean. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
I suggest you read the original paper for Martini Protein FF. I think it is not suitable for your purpouse. 2009/12/17 rasoul nasiri nasiri1...@gmail.com Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are beads of protein from water beads with suitable van der wall distance (larger than 0.105nm), when I want to start production phase, first switch back to the smaller radius of van der waals of the water beads, then I will continue CGMD simulation. Is it possible I reduce this radius? Which commands of Gromacs suit can do it? Rasoul On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: rasoul nasiri wrote: greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? Read up on your forcefield and find out how large the particles tend to be. It only has to be good enough, not perfect. I have to switch back to the smaller radius afterward, Is it correct? Changing what for what purpose? if yes, How can I do it? I tried with editconf but could not. I don't know what you mean. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
yes, I know there will be limitation for modeling of Folding/Unfolding proteins with MARtini CGFF if I want to look at complete folding/unfolding mechanism of proteins but I want to find out localized regions of the protein (e.g. the C- or N-termini) that they have contribution to the denaturation mechanism. My question is about vdwd in beads of water. Is it OK if I select distances of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I have to reconstruct the system in smaller vdw distance of the water beads for doing my purpose. and Which commands of Gromacs can do it? Best regards Rasoul On Thu, Dec 17, 2009 at 5:03 PM, César Ávila clav...@gmail.com wrote: I suggest you read the original paper for Martini Protein FF. I think it is not suitable for your purpouse. 2009/12/17 rasoul nasiri nasiri1...@gmail.com Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are beads of protein from water beads with suitable van der wall distance (larger than 0.105nm), when I want to start production phase, first switch back to the smaller radius of van der waals of the water beads, then I will continue CGMD simulation. Is it possible I reduce this radius? Which commands of Gromacs suit can do it? Rasoul On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: rasoul nasiri wrote: greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? Read up on your forcefield and find out how large the particles tend to be. It only has to be good enough, not perfect. I have to switch back to the smaller radius afterward, Is it correct? Changing what for what purpose? if yes, How can I do it? I tried with editconf but could not. I don't know what you mean. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] the resource of Vdw Radii in Vdwradii.dat
Hi all I am a new in using Gromacs 4 I now using g_sas to calculate the solvent accessible surface. Yet, the outcome informs me the Vdw radius is missing for P atom in Vdwradii.dat. Thus I check the file and want to add the value for P. However, though I read through the Manual, I can not find the reference of the source of the values in Vdwradii.dat. Could some one tell me which paper these radius in Vdwradii.dat come from? Thanks Huikuan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
rasoul nasiri wrote: yes, I know there will be limitation for modeling of Folding/Unfolding proteins with MARtini CGFF if I want to look at complete folding/unfolding mechanism of proteins but I want to find out localized regions of the protein (e.g. the C- or N-termini) that they have contribution to the denaturation mechanism. My question is about vdwd in beads of water. Is it OK if I select distances of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I have to reconstruct the system in smaller vdw distance of the water beads for doing my purpose. and Which commands of Gromacs can do it? The values in vdwradii.dat are not used in the actual simulation. They are used by tools like editconf and genbox when building the system. Attractive and repulsive parameters for nonbonded interactions are defined by the force field, which is assembled in the input to mdrun. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] the resource of Vdw Radii in Vdwradii.dat
On 12/17/09 5:43 PM, huikuan chao wrote: Hi all I am a new in using Gromacs 4 I now using g_sas to calculate the solvent accessible surface. Yet, the outcome informs me the Vdw radius is missing for P atom in Vdwradii.dat. Thus I check the file and want to add the value for P. However, though I read through the Manual, I can not find the reference of the source of the values in Vdwradii.dat. Could some one tell me which paper these radius in Vdwradii.dat come from? Thanks Huikuan Unfortunately there is no ref. But you can easily add your own favorite values. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://xray.bmc.uu.se/~spoel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] How is calculated the bind free energy GROMACS???
Hi, I need to know how to calculated GROMACS, the bind free energy, words, equations used to calculated the bind free energy in the sub-program g_lie. Thank you Deisy Y. Rodriguez S. Practicante de Computos Avanzados Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX Tel. 6344000 ext. 2792 Universidad Industrial de Santander -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 68, Issue 86
Hi All: I just wanted to add my 2 cents to the already excellent comments posted about the conversion of different types of ion Lennard-Jones parameters, since I get lots of emails about this very subject. It is misleading to think of an ion parameter as a SINGLE value of sigma and epsilon. The combination rules are a sort of shorthand, what was actually parametrized were PAIRS of lennard-jones interactions between ions and various other particles. So in any attempt to transplant parameters from one convention to another, at a minimum, one must refer to the original parametrization literature to see precisely which interactions must be preserved (via specific overrides in a topology or FF .itp file). For all ion parameters, this definitely includes the ion-water interaction, since this determines the free energy of solvation. In the case of the Cheatham Young ions, the motivation for these parameters was to avoid crystallization artifacts caused by anomalously short cation-anion distances, which was alleviated by including the crystal lattice as part of the parametrization, therefore the cation-anion interaction parameter must also be overridden. The sigma primes that are mentioned are derivable using very simple algebra, just by setting the sigma for a particular interaction PAIR to be equal under both mixing rules, and solving for sigma prime. For example, here is a description of how Aqvist's ions were transplanted into AMBER (note that this description is slightly more complicated because of a conversion from R* to sigma, and that TIP3P O sigmas are identical in either combination rule). http://ambermd.org/Questions/vdw.html (Note that this only preserves one particular interaction PAIR, you would have to repeat this process for any additional interactions in your simulation unless you are simulating only ions and water.) But just because you CAN do this doesn't mean it's a good idea. In principle, one would have to override every possible pair interaction with the transplanted ion using the mixing rules appropriate to the ion. Even then, you have no guarantees that any interaction that was not explicitly part of the parametrization process are sane or correct, both because the new force field likely uses different charges and L-J parameters for equivalent biomolecular atoms, and because you have no guarantee that these interactions were at all validated even in the original force field unless it was part of the parametrization process. Practically speaking, however, it is only the water and highly charged moieties that one will need to pay particular attention to, but my point is that this should always be done with great care, since small inaccuracies in transplanting ion parameters can have dramatically bad results due to the large energies involved (see Cheatham Young's original report or my own in http://pubs.acs.org/doi/abs/10.1021/jp0765392). Cheers, Alan Chen postdoctoral research associate - Garcia Group Rensselaer Polytechnic Institute, Troy NY che...@rpi.edu On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] Re: sulfate atomtype for ffgmx (Justin A. Lemkul)
Thank you both for the suggestions. My system does also contain carbohydrates (sugar) and ffoplsaa.atp does not contain the atomtypes for these molecules. Even though carbohydrate parameters have been published for OPLS they are not present in the ffoplsaa.atp file. I did look into the available atomtypes in all the force fields in the downloaded GROMACS package (4.0.5) and the one that has most of the molecules I require is ffgmx. Perhaps the GROMOS force fields can be used as well allthough they dont have seperate sugar atomtypes (CH2 = aliphatic or sugar carbon), or the porphyrin N that is also present in my simulation. The Sulfate is also missing in GROMOS. That was the reason why I finally ended up with the decrapetated ffgmx, because it contains all but one specific atomtype I require. Should I prevent using ffgmx completely since it is decrapetated? Can the OPLS-AA carbohydrate parameters be ported to GROMACS? Or is it better to try and run my system in a different MD package that contains all specific atomtypes? Michiel _ Niesen, Michiel wrote: Dear all, I would like to perform MD simulations on a molecule that contains a carbon chain with a sulfonyl (R-SO2-R) group in between. When looking at the available atomtypes for ffgmx I didnt find a sulfate S. Only sulfur (S) and DMSO sulphur atomtypes are available. In literature I did find GROMACS simulations performed on systems with a sulfate group but all of them used the standard Sulfur atomtype. If there is precedent, you may be able to use it. However, you should be warned that ffgmx is considered a deprecated force field, and in the absence of a very compelling reason to use it, probably isn't a wise choice. There are many (newer) versions of Gromos force fields that are probably more reliable. So my question; Would it be reasonable to use the sulfur atomtype for a sulfonyl group R-SO2-R? (as done previously in literature) If not, is there a sulfate atomtype available for ffgmx or would you recommend me to use another force field such as CHARMM for this system? There are numerous sulfur atom types in OPLS-AA that may be usable. Have a look at the .atp file to see. CHARMM is not yet officially supported in Gromacs, so that force field probably isn't a viable option. -Justin Kind regards, Michiel _ ffgmx is deprecated, so the answer is use another force field. In general it is not reasonable to use an atom type in a functional group that differs markedly from that it which it was parameterized. Mark _ - SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] error with changing pdb file
Hello, While I am simulating my simulations, I encountered below error. I have pdb file which is: HEADERPROTEINTITLE (5,5) Nanotube (1,1,80) replicationAUTHORTubeGen 3.3, J T Frey, University of DelawareEXPDTATHEORETICAL MODELATOM 1 C UNK 1 3.410 0.000 -98.494 1.00 0.00ATOM 2 C UNK 1 3.113 1.390 -98.494 1.00 0.00ATOM 3 C UNK 1 2.758 2.004 -97.263 1.00 0.00ATOM 4 C UNK 1 1.702 2.954 -97.263 1.00 0.00ATOM 5 C UNK 1 1.054 3.243 -98.494 1.00 0.00ATOM 6 C UNK 1 -0.360 3.391 -98.494 1.00 0.00ATOM 7 C UNK 1 -1.054 3.243 -97.263 1.00 0.00ATOM 8 C UNK 1 -2.284 2.532 -97.263 1.00 0.00ATOM 9 C UNK 1 -2.758 2.004 -98.494 1.00 0.00... CONECT 1596 1595 1597CONECT 1597 1576 1596 1598CONECT 1598 1579 1597 1599CONECT 1599 1598 1600CONECT 1600 1581 1599MASTER000000 00 16000 16000END But by using text editor, I change an atom with another atom.And I created .top and .gro files respectively.( my sample is basically similar to Christopher Stiles' work, http://cs86.com/CNSE/SWNT.htm) After I run my simulation, it gives the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#checking input for internal consistency...calling cpp...processing topology...Generated 1282 of the 1485 non-bonded parameter combinationsWARNING 1 [file cnt_500.top, line 72238]: No default Angle types, using zeroesWARNING 2 [file cnt_500.top, line 72238]: No default Angle types for perturbed atoms, using normal valuesWARNING 3 [file cnt_500.top, line 72239]: No default Angle types, using zeroesWARNING 4 [file cnt_500.top, line 72239]: No default Angle types for perturbed atoms, using normal valuesWARNING 5 [file cnt_500.top, line 72240]: No default Angle types, using zeroesWARNING 6 [file cnt_500.top, line 72240]: No default Angle types for perturbed atoms, using normal valuesWARNING 7 [file cnt_500.top, line 72241]: No default Angle types, using zeroesWARNING 8 [file cnt_500.top, line 72241]: No default Angle types for perturbed atoms, using normal valuesWARNING 9 [file cnt_500.top, line 72242]: No default Angle types, using zeroesWARNING 10 [file cnt_500.top, line 72242]: No default Angle types for perturbed atoms, using normal valuesCleaning up temporary file gromppYFxvHw---Program grompp_mpi, VERSION 3.3.1Source code file: fatal.c, line: 416 Fatal error:Too many warnings, grompp_mpi terminated--- Without changing my pdb file, there was no error but after I can an atom with another, I got above error.Is there anyone who had same problem before? I will really appreciate if you can help me. Thank you,Kasim _ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] error with changing pdb file
ksm tprk wrote: Hello, While I am simulating my simulations, I encountered below error. I have pdb file which is: HEADERPROTEIN TITLE (5,5) Nanotube (1,1,80) replication AUTHORTubeGen 3.3, J T Frey, University of Delaware EXPDTATHEORETICAL MODEL ATOM 1 C UNK 1 3.410 0.000 -98.494 1.00 0.00 ATOM 2 C UNK 1 3.113 1.390 -98.494 1.00 0.00 ATOM 3 C UNK 1 2.758 2.004 -97.263 1.00 0.00 ATOM 4 C UNK 1 1.702 2.954 -97.263 1.00 0.00 ATOM 5 C UNK 1 1.054 3.243 -98.494 1.00 0.00 ATOM 6 C UNK 1 -0.360 3.391 -98.494 1.00 0.00 ATOM 7 C UNK 1 -1.054 3.243 -97.263 1.00 0.00 ATOM 8 C UNK 1 -2.284 2.532 -97.263 1.00 0.00 ATOM 9 C UNK 1 -2.758 2.004 -98.494 1.00 0.00 ... CONECT 1596 1595 1597 CONECT 1597 1576 1596 1598 CONECT 1598 1579 1597 1599 CONECT 1599 1598 1600 CONECT 1600 1581 1599 MASTER00000000 16000 16000 END But by using text editor, I change an atom with another atom. And I created .top and .gro files respectively. ( my sample is basically similar to Christopher Stiles' work, http://cs86.com/CNSE/SWNT.htm) After I run my simulation, it gives the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling cpp... processing topology... Generated 1282 of the 1485 non-bonded parameter combinations WARNING 1 [file cnt_500.top, line 72238]: No default Angle types, using zeroes WARNING 2 [file cnt_500.top, line 72238]: No default Angle types for perturbed atoms, using normal values WARNING 3 [file cnt_500.top, line 72239]: No default Angle types, using zeroes WARNING 4 [file cnt_500.top, line 72239]: No default Angle types for perturbed atoms, using normal values WARNING 5 [file cnt_500.top, line 72240]: No default Angle types, using zeroes WARNING 6 [file cnt_500.top, line 72240]: No default Angle types for perturbed atoms, using normal values WARNING 7 [file cnt_500.top, line 72241]: No default Angle types, using zeroes WARNING 8 [file cnt_500.top, line 72241]: No default Angle types for perturbed atoms, using normal values WARNING 9 [file cnt_500.top, line 72242]: No default Angle types, using zeroes WARNING 10 [file cnt_500.top, line 72242]: No default Angle types for perturbed atoms, using normal values Cleaning up temporary file gromppYFxvHw --- Program grompp_mpi, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp_mpi terminated --- Without changing my pdb file, there was no error but after I can an atom with another, I got above error. Is there anyone who had same problem before? I will really appreciate if you can help me. If you have altered the atom numbers or types without re-generating the topology, then the angles in the topology will no longer make sense. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] LIE precision and accuracy
Hello, I am in the middle of using Gromacs 3.3.3 to evaulate interaction energies between a protein and two separate ligands to compare their binding affinities. In doing this I have run each solvated complex through a 1 ns MD simulation and each solvated ligand through a 1 ns MD simulation. After the trajectories were complete, I ran g_lie on the trajectories for each case. Next, I subtracted the average ligand LIE from the average complex LIE for each case to get the interaction energy . Data is as follows: Ligand 1 Ligand 2 LIE (kcal/mol) -5.7 -8.9 St dev. 6.7 4.7 While the average energies themselves are reasonable, the st dev's seem to me to be too large - rendering the energy difference meaningless. I calculated the st. dev's based on the trajectories' g_lie values (in this case 1000 data points for a 1 ns run). I read in the tutorials that PME condition should not be used with g_lie, so I switched to cut-offs for my electrostatic forces. Is there anything else I might be missing? Again, I know the st. dev's are just too high to make g_lie useful so I blame myself for the initial setup. My .mdp file is below. Thanks, Marc ; mdrun for C4AHL on unix parameters title = trp_drg MD cpp = /usr/bin/cpp ; location of cpp on linux constraints = all-bonds integrator = md dt = 0.002 ; ps! nsteps = 50 ; total 1000 ps nstcomm = 1 nstxout = 500 ; output coords every 1 ps nstvout = 0 nstfout = 0 nstenergy = 500 nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 coulombtype = cut-off rcoulomb = 1.2 vdwtype = cut-off rvdw = 1.4 ;fourierspacing = 0.12 ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 6 ;ewald_rtol = 1e-5 ;optimize_fft = yes ; Berendsen temperature coupling is on in five groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Use Energy group monitoring energygrps = protein C6L OHY SOL Na+ ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is on at 300 K gen_vel = yes gen_temp = 300.0 gen_seed = -1 free_energy = yes-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] error with changing pdb file
ksm tprk wrote: I changed pdb file after that I generated topology file. It appears you are relying on grompp to figure out what parameters should be used for these angles, and apparently, given these atom types, there are no default values available in the force field you've chosen to use. So either specify parameters manually or use a different force field. If you need further advice, it would be useful to know the force field you're trying to use and see the problematic lines of the topology alongside the modified coordinate file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] LIE precision and accuracy
On 12/17/09 9:24 PM, Marc Charendoff wrote: Hello, I am in the middle of using Gromacs 3.3.3 to evaulate interaction energies between a protein and two separate ligands to compare their binding affinities. In doing this I have run each solvated complex through a 1 ns MD simulation and each solvated ligand through a 1 ns MD simulation. After the trajectories were complete, I ran g_lie on the trajectories for each case. Next, I subtracted the average ligand LIE from the average complex LIE for each case to get the interaction energy . Data is as follows: *Ligand 1* *Ligand 2* *LIE (kcal/mol)* -5.7-8.9 *St dev.* 6.7 4.7 While the average energies themselves are reasonable, the st dev's seem to me to be too large - rendering the energy difference meaningless. I calculated the st. dev's based on the trajectories' g_lie values (in this case 1000 data points for a 1 ns run). I read in the tutorials that PME condition should not be used with g_lie, so I switched to cut-offs for my electrostatic forces. Is there anything else I might be missing? Again, I know the st. dev's are just too high to make g_lie useful so I blame myself for the initial setup. My .mdp file is below. Cut-off should not be used either :). You can estimate the error rather than std. dev. using g_analyze -ee Thanks, Marc ; mdrun for C4AHL on unix parameters title = trp_drg MD cpp = /usr/bin/cpp ; location of cpp on linux constraints = all-bonds integrator = md dt = 0.002 ; ps! nsteps = 50 ; total 1000 ps nstcomm = 1 nstxout = 500 ; output coords every 1 ps nstvout = 0 nstfout = 0 nstenergy = 500 nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 coulombtype = cut-off rcoulomb = 1.2 vdwtype = cut-off rvdw = 1.4 ;fourierspacing = 0.12 ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 6 ;ewald_rtol = 1e-5 ;optimize_fft = yes ; Berendsen temperature coupling is on in five groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Use Energy group monitoring energygrps = protein C6L OHY SOL Na+ ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is on at 300 K gen_vel = yes gen_temp = 300.0 gen_seed = -1 free_energy = yes -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://xray.bmc.uu.se/~spoel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] LIE precision and accuracy
In spite of the fact that I have never used g_lie, I have used a variety of different techniques to calculate binding free energies, and I would be astounded if it was possible to get the precision that you desire with only 1 ns of sampling per state. Are you sure that the reported imprecision is different from the actual imprecision obtained via 1 ns of sampling? Generally, one evaluates the convergence by block averaging or some other convergence indicator. If you do find a measure by which your precision is reported to be very good, then I would suspect that your sampling is trapped and that your free energies are not accurate in any event. In short, I think that your comment about rendering the energy difference meaningless is actually quite astute. Chris. -- original message -- Hello, I am in the middle of using Gromacs 3.3.3 to evaulate interaction energies between a protein and two separate ligands to compare their binding affinities. In doing this I have run each solvated complex through a 1 ns MD simulation and each solvated ligand through a 1 ns MD simulation. After the trajectories were complete, I ran g_lie on the trajectories for each case. Next, I subtracted the average ligand LIE from the average complex LIE for each case to get the interaction energy . Data is as follows: Ligand 1 Ligand 2 LIE (kcal/mol) -5.7 -8.9 St dev.6.74.7 While the average energies themselves are reasonable, the st dev's seem to me to be too large - rendering the energy difference meaningless. I calculated the st. dev's based on the trajectories' g_lie values (in this case 1000 data points for a 1 ns run). I read in the tutorials that PME condition should not be used with g_lie, so I switched to cut-offs for my electrostatic forces. Is there anything else I might be missing? Again, I know the st. dev's are just too high to make g_lie useful so I blame myself for the initial setup. My .mdp file is below. Thanks, Marc ; mdrun for C4AHL on unix parameters title = trp_drg MD cpp = /usr/bin/cpp ; location of cpp on linux constraints = all-bonds integrator = md dt = 0.002 ; ps! nsteps = 50 ; total 1000 ps nstcomm = 1 nstxout = 500 ; output coords every 1 ps nstvout = 0 nstfout = 0 nstenergy = 500 nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 coulombtype = cut-off rcoulomb = 1.2 vdwtype = cut-off rvdw = 1.4 ;fourierspacing = 0.12 ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 6 ;ewald_rtol = 1e-5 ;optimize_fft = yes ; Berendsen temperature coupling is on in five groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 300 300 ; Use Energy group monitoring energygrps = protein C6L OHY SOL Na+ ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is on at 300 K gen_vel = yes gen_temp = 300.0 gen_seed = -1 free_energy = yes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] error with changing pdb file
ksm tprk wrote: Hello Justin, I looked at in my gromacs/3.3.1 and it ahs only ffgmx.n2t force field file. because of that, I chaged to new version gromacs. I tried to use different force filed but new version gromacs but they didn't work. I used gromacs/4.0.5 and I created .gro and by using x2top but it give below errors. If I use pdb2gmx, it gives me residue UNK error. First I used GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) but it gave me below error: Can not find forcefield for atom C-1597 with 3 bonds Can not find forcefield for atom C-1598 with 3 bonds Can not find forcefield for atom C-1599 with 2 bonds Can not find forcefield for atom C-1600 with 2 bonds --- Program x2top_mpi, VERSION 4.0.5 Source code file: x2top.c, line: 207 Fatal error: Could only find a forcefield type for 0 out of 1600 atoms --- After that I used OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) and it gave me: Looking whether force field files exist Opening library file /opt/apps/gromacs/4.0.5/share/gromacs/top/ffoplsaa.rtp Opening library file ffoplsaa.n2t Opening library file ffoplsaa.n2t There are 25 name to type translations Generating bonds from distances... atom 1600 Can not find forcefield for atom N-25 with 3 bonds --- Program x2top_mpi, VERSION 4.0.5 Source code file: x2top.c, line: 207 Fatal error: Could only find a forcefield type for 1599 out of 1600 atoms --- And I tried [DEPRECATED] Gromacs force field (see manual) and Encad all-atom force field, using scaled-down vacuum charges. they gave me same error at first. The 4.0.5 version of x2top is broken unless you use the -nopbc option, which, for the purposes of carbon nanotubes, is useless unless you specify all the cross-boundary bonded terms yourself. You had a functional topology before, why are you starting over? You didn't give a very clear description of the changes you were making that were inducing the grompp errors, and you stand a better chance of identifying those problems and solving them if you provide the information I asked for last time (relevant topology lines and the corresponding coordinate entries). -Justin Thank you, Kasim Date: Thu, 17 Dec 2009 15:31:23 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] error with changing pdb file ksm tprk wrote: I changed pdb file after that I generated topology file. It appears you are relying on grompp to figure out what parameters should be used for these angles, and apparently, given these atom types, there are no default values available in the force field you've chosen to use. So either specify parameters manually or use a different force field. If you need further advice, it would be useful to know the force field you're trying to use and see the problematic lines of the topology alongside the modified coordinate file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php Hotmail: Powerful Free email with security by Microsoft. Get it now. http://clk.atdmt.com/GBL/go/171222986/direct/01/ -- 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/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/mailing_lists/users.php
[gmx-users] trjcat error
Hi ALL, I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water simulation. I am using trjcat to join them into a single .trr file for analysis and getting the following error: --- Continue writing frames from PRO_10_NS.part0003.trr t=4604 ps, frame=2302 - frame 3990 time 7980.000 ps - frame 3910 time 7820.000 ps --- Program trjcat, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file What should I do? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] trjcat error
Hi Anirban, Check each trajectory with gmxcheck to see whether they are okay. Cheers, Tsjerk On Fri, Dec 18, 2009 at 7:32 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water simulation. I am using trjcat to join them into a single .trr file for analysis and getting the following error: --- Continue writing frames from PRO_10_NS.part0003.trr t=4604 ps, frame=2302 - frame 3990 time 7980.000 ps - frame 3910 time 7820.000 ps --- Program trjcat, VERSION 4.0.5 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file What should I do? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
