Re: [gmx-users] question about force field parameter
On Sun, May 24, 2009 at 8:42 AM, Mark Abraham wrote: > > > ; -CH2-S- 0.7 >> > > This is a comment line. > > What's the meaning of the number 0.7 in this comment line? Thanks! Yan ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] question about force field parameter
Yan Chai wrote: On Sun, May 24, 2009 at 8:42 AM, Mark Abraham wrote: ; -CH2-S- 0.7 This is a comment line. What's the meaning of the number 0.7 in this comment line? I don't know. Nobody would be likely to know without knowing the full context, which nobody has bothered to provide or describe. Even then, maybe only the person who wrote it might know. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] question about force field parameter
Mark Abraham wrote: Yan Chai wrote: On Sun, May 24, 2009 at 8:42 AM, Mark Abraham wrote: ; -CH2-S- 0.7 This is a comment line. What's the meaning of the number 0.7 in this comment line? multiply by 4.184 I don't know. Nobody would be likely to know without knowing the full context, which nobody has bothered to provide or describe. Even then, maybe only the person who wrote it might know. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] question about force field parameter
Excuse me, I don't understand. Could you please explain more in details on this? What do you mean to multiply by 4.184? I have seen many similar numbers following the examples of bonds in the comment lines in the force field files, but I never understood them. Thanks! Yan On Sun, May 24, 2009 at 10:34 AM, David van der Spoel wrote: > Mark Abraham wrote: > >> Yan Chai wrote: >> >>> On Sun, May 24, 2009 at 8:42 AM, Mark Abraham wrote: >>> >>> >>> >>>; -CH2-S- 0.7 >>> >>> >>>This is a comment line. >>> >>> >>> >>> What's the meaning of the number 0.7 in this comment line? >>> >> multiply by 4.184 > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] question about force field parameter
Yan Chai wrote: Excuse me, I don't understand. Could you please explain more in details on this? What do you mean to multiply by 4.184? I have seen many similar numbers following the examples of bonds in the comment lines in the force field files, but I never understood them. calories to joules Thanks! Yan On Sun, May 24, 2009 at 10:34 AM, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote: Mark Abraham wrote: Yan Chai wrote: On Sun, May 24, 2009 at 8:42 AM, Mark Abraham wrote: ; -CH2-S- 0.7 This is a comment line. What's the meaning of the number 0.7 in this comment line? multiply by 4.184 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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: question about force field parameter
The reason I asked the question was becuase I was trying to understand them in order to parameterize some bonds myself. for example, dihedral angles a lot time are clearly commented, so I know which bonds could use the parameter. e.g. #define gd_4180.000 5.86 1 ; N-CHn-CHn-OA (lipid) 1.4 ; #define gd_5180.000 9.35 1 ; OA-CHn-CHn-OA (sugar) 2.2 But those like following is comfusing to me which conditions they are discribing since it commented 2 atoms for a dihedral angle #define gd_38 0.0000.0 4 ; -NR-FE- 0.0 ; #define gd_39 180.0001.0 6 ; -CHn-N,NE-0.24 ; #define gd_40 0.0001.0 6 ; -CHn-C,NR(ring), CR1- 0.24 ; thanks Johnny Message: 5 Date: Sun, 24 May 2009 16:42:35 +1000 From: Mark Abraham Subject: Re: [gmx-users] question about force field parameter To: Discussion list for GROMACS users Message-ID: <4a18ec5b.6060...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Zhanglin Ni wrote: Dear all I am a little confused with some force field parameter library. for example Whether and how this makes sense depends on the context, which you need to tell us, since we are not going to go looking and guessing for you. :-) #define gd_26 0.000 2.93 3 This defines a preprocessor macro called gd_26 that replaces each instance of that token string with the three numbers above. ; -CH2-S- 0.7 This is a comment line. dihedral is supposed to be i j k l 4 atoms , why, for example, the case above has only 2 atoms. You may need to consider the effect of that macro in the context where it is used. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 to solve the warning
hi,gmx-user I make a molecule *.itp and force field parameters. When I run editconf and genbox to build a system,there are always a warning like this. "Warning: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type." I don't know how to solve the problem. Jinyao Wang wan...@ciac.jl.cn 2009-05-25 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 to solve the warning
Jinyao Wang wrote: > hi,gmx-user > > I make a molecule *.itp and force field parameters. When I run editconf and > genbox to build a system,there are always a warning like this. "Warning: > masses will be determined based on residue and atom names, this can deviate > from the real mass of the atom type." > > I don't know how to solve the problem. This is normal output. It is probably only relevant if doing more advanced tricks with editconf, like -princ. For normal preparation of a box, there should be no problem. -Justin > > Jinyao Wang wan...@ciac.jl.cn 2009-05-25 > > > > > ___ gmx-users mailing list > gmx-users@gromacs.org http://www.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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://www.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] charge distribution
Hi all, I am using g_potential to calculate the charge distribution of my system which consists of a protein layer covalently bound to some fatty acids. The protein layer by itself would have an overall negative charge but they system as a whole is neutral. My question is this: When I specify different values for the number of slices, and I sum up the charges for the protein only, I always get different results with different number of slices. But shouldn't the overall charge of the protein layer be the same regardless of the number of slices or the size of each bin? The difference is also quite significant so I don't think it is simply a rounding error. For example with a 0.1 nm bin width, I get an overall charge of -3, but with a bin width of 0.05nm, the overall charge is -7. Could someone possibly explain to me what is going on? Thanks! This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Re: question about force field parameter
Hi Johnny, If for a dihedral the definition only lists two atoms, these signify the central atoms with any possible substituents. I think this is explained in Chapter 5 of the manual. Cheers, Tsjerk On Sun, May 24, 2009 at 5:58 PM, Zhanglin Ni wrote: > The reason I asked the question was becuase I was trying to understand them > in order to parameterize some bonds myself. > for example, dihedral angles a lot time are clearly commented, so I know > which bonds could use the parameter. > e.g. > #define gd_4 180.000 5.86 1 > ; N-CHn-CHn-OA (lipid) 1.4 > ; > #define gd_5 180.000 9.35 1 > ; OA-CHn-CHn-OA (sugar) 2.2 > > But those like following is comfusing to me which conditions they are > discribing since it commented 2 atoms for a dihedral angle > #define gd_38 0.000 0.0 4 > ; -NR-FE- 0.0 > ; > #define gd_39 180.000 1.0 6 > ; -CHn-N,NE- 0.24 > ; > #define gd_40 0.000 1.0 6 > ; -CHn-C,NR(ring), CR1- 0.24 > ; > > > thanks > Johnny >> >> Message: 5 >> Date: Sun, 24 May 2009 16:42:35 +1000 >> From: Mark Abraham >> Subject: Re: [gmx-users] question about force field parameter >> To: Discussion list for GROMACS users >> Message-ID: <4a18ec5b.6060...@anu.edu.au> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Zhanglin Ni wrote: >>> >>> Dear all >>> I am a little confused with some force field parameter library. for >>> example >> >> Whether and how this makes sense depends on the context, which you need >> to tell us, since we are not going to go looking and guessing for you. :-) >> >>> #define gd_26 0.000 2.93 3 >> >> This defines a preprocessor macro called gd_26 that replaces each >> instance of that token string with the three numbers above. >> >>> ; -CH2-S- 0.7 >> >> This is a comment line. >> >>> dihedral is supposed to be i j k l 4 atoms , why, for example, the case >>> above has only 2 atoms. >> >> You may need to consider the effect of that macro in the context where >> it is used. >> >> Mark >> >> >>> > > ___ > gmx-users mailing list gmx-us...@gromacs.org > http://www.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. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 default pH =7.0 ??? and the protonation state after pdb2gmx
Hi I am a bit confused. 1LW9.pdb = T4 lysozyme After this command, pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top => GG 45a3is choosed. The Gromacs tells me that it carries +8 charges. As we know, that the amount of charges which the protein carries is based on pH values. So, my question is this command => pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top at what condition Gromacs calculate the charges of the protein?? Thank you Lin Chih-Ying Lin wrote: > Hi > after the command pdb2gmx, > the protein will be added appropriate H, > > So, does pdb2gmx add H (protonate) based on pH =7.0 ? No. You should choose the protonation state based on your understanding of the conditions you wish to model, and instruct pdb2gmx accordingly. Read pdb2gmx -h. Do some tutorials - this sort of thing is covered there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 default pH =7.0 ??? and the protonation state after pdb2gmx
Lin, Gromacs isn't choosing a specific condition, but rather it building the protein using a set of defaults. Try looking at the documentation for pdb2gmx, which clearly states the defaults that the program uses for assigning the protonation state of the residues of interest. Given those defaults, you need to decide if they are appropriate for the conditions you are trying to simulate, and if not, you need to change them accordingly. Josh On May 24, 2009, at 11:37 PM, Chih-Ying Lin wrote: Hi I am a bit confused. 1LW9.pdb = T4 lysozyme After this command, pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top => GG 45a3is choosed. The Gromacs tells me that it carries +8 charges. As we know, that the amount of charges which the protein carries is based on pH values. So, my question is this command => pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top at what condition Gromacs calculate the charges of the protein?? Thank you Lin Chih-Ying Lin wrote: Hi after the command pdb2gmx, the protein will be added appropriate H, So, does pdb2gmx add H (protonate) based on pH =7.0 ? No. You should choose the protonation state based on your understanding of the conditions you wish to model, and instruct pdb2gmx accordingly. Read pdb2gmx -h. Do some tutorials - this sort of thing is covered there. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- Joshua L. Adelman Biophysics Graduate Group Lab: 510.643.2159 218 Wellman HallFax: 510.642.7428 University of California, Berkeley http://nature.berkeley.edu/ ~jadelman Berkeley, CA 94720 USA jadel...@berkeley.edu -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 default pH =7.0 ??? and the protonation state after pdb2gmx
Hi Lin, Please follow the advice to do more background reading on both biochemistry and molecular dynamics if you aren't doing so already. The charge is not related to the pH. pH is related to the concentration of H+ in the solution, but you don't have H+ (H3O+/OH-) in your solution. The charge is what you determine it to be. You specify that an asparagine is protonated or not, and specify whether a histidine is protonated at Nd, Ne, both or none. You can make whatever choice you want, although these are not equally meaningful. If you don't explicitly specify protonation states, pdb2gmx will simple take the most common one for an amino acid free in solvent at pH 7: Asp and Glu deprotonated, Lys protonated... This has nothing to do with the expected protonation state of a protein at a certain pH. Mind that the computer doesn't think for you. It makes choices for you, and that can be a serious source of error. The computer lacks insight and chemical intuition. You'll have to provide that. That's why you have to make sure you're skilled enough in terms of the theoretical background. Cheers, Tsjerk On Mon, May 25, 2009 at 8:37 AM, Chih-Ying Lin wrote: > Hi > I am a bit confused. > 1LW9.pdb = T4 lysozyme > > After this command, > pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top > > => GG 45a3 is choosed. > > The Gromacs tells me that it carries +8 charges. > > > > As we know, that the amount of charges which the protein carries is > based on pH values. So, my question is > > this command => > pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top > at what condition Gromacs calculate the charges of the protein?? > > > > Thank you > Lin > > > > > > > > > Chih-Ying Lin wrote: >> Hi >> after the command pdb2gmx, >> the protein will be added appropriate H, >> >> So, does pdb2gmx add H (protonate) based on pH =7.0 ? > > No. You should choose the protonation state based on your understanding > of the conditions you wish to model, and instruct pdb2gmx accordingly. > Read pdb2gmx -h. Do some tutorials - this sort of thing is covered there. > > Mark > ___ > gmx-users mailing list gmx-us...@gromacs.org > http://www.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. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Installing topolbuild
Hi Bruce, I was trying to generate topologies for one ligand using topolbuild. For the same I used the command "*topolbuild -dir /home/vivek/topolbuild1_2_1/dat/gromacs/ -ff gmx43a1 -n Bromo-WR99210 -r RESID*" and it resulted in an error as follow: *Fatal error. Source code file: readmol2.c, line: 580 Bond record does not end with another mol2 record type entry. >From the error it suggest some problem with the input .mo2 format. Here I am attaching the **Bromo-WR99210.mol2 *file, which I used as input. Please suggest/correct if I am doing some mistake in command line or I am missing something. Thanks in advance. ~Vivek 2009/4/16 Bruce D. Ray > Apparently some versions of make do not handle my make files the same way > that > the version of make I use does. The attached Makefile might help in such > cases. > > > Sincerely, > > -- > Bruce D. Ray, Ph.D. > Associate Scientist, and Operations Director > NMR Center > IUPUI > Physics Dept. > 402 N. Blackford St. > Indianapolis, IN 46202-3273 > > > -- > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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://www.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
