Re: [gmx-users] free energy and charges
parto haghighi wrote: Dear GMX users, when I want to correct charge group of one molecule I have to do calculate its free energy. I did this work by applying 6th gromacs tutorial. In this tutorial user has to assign 0 value in topology: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_138 1 ALAB CB 1 0.000 12.011 2 opls_140 1 ALABHB1 2 0.000 1.008 3 opls_140 1 ALABHB2 3 0.000 1.008 4 opls_140 1 ALABHB3 4 0.000 1.008 5 opls_140 1 ALABHB4 5 0.000 1.008 my question is when I have to zero value to its charge how can I correct my charges: Don't set your charges to zero. The tutorial states why everything is zero there - the process for which the free energy calculation is being done is a van der Waals transformation, so the charges are fixed at zero. For your calculations, you need to: 1. assign some starting value for charges (QM, chemical intuition, etc) and atom types 2. calculate DG of solvation and check the accuracy of the resulting value 3. adjust charges (and perhaps atom types) if necessary and return to step 1 -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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] copper and His residues
Hello, I am a beginner of Gromacs, and I am working with enzyme that contains two Cu2+ ions in the active site. I have found two solution to treat copper ions and surrounding His residues. First solution is adding position restrain to these ions, while the second one is defining bonds between copper ions and surrounding His residues. I just wonder about which one should I adopt? Thanks very much. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] combining umbrella sampling with replica exchange
Hi, I sent this email few weeks back and thought sending it again in case someone can give some opinion. I have a technical question regarding feasibility of combining replica exchange with umbrella sampling or any other pulling simulations in gromacs. Since the umbrella sampling or any other pulling simulations are non-equilibrium simulation due to presence of external bias, I wonder whether the detailed balance in replica exchange simulation will be maintained . I ask this because replica exchange uses Monte Carlo metropolis algorithm to swap configurations and so I wanted to know what is the energy-difference ( New energy - old energy) in metropolis algorithm gromacs will use : Is it the energy difference after taking into account the biasing potential or is is only the internal potential energy-difference ( i.e not including biasing potential ) ? Any response from the users or developer will be highly appreciated. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] make error Makefile:347: recipe for target `all-recursive' failed for Gromacs-4.5.5
Hi Mark (and all) Thanks for the response. I ran ./configure --disable-threads this time. ./configure went fine but again upon doing Make I have received a new error: Creating library file: .libs/libmd.dll.a .libs/fft5d.o:fft5d.c:(.text+0x140f): undefined reference to `_fftwf_plan_guru_d ft' .libs/fft5d.o:fft5d.c:(.text+0x18d1): undefined reference to `_fftwf_plan_guru_d ft_r2c' .libs/fft5d.o:fft5d.c:(.text+0x194b): undefined reference to `_fftwf_plan_guru_d ft_c2r' .libs/fft5d.o:fft5d.c:(.text+0x1aef): undefined reference to `_fftwf_execute' .libs/fft5d.o:fft5d.c:(.text+0x2133): undefined reference to `_fftwf_execute' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x4a): undefined reference to `_fft wf_malloc' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x67): undefined reference to `_fft wf_malloc' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x84): undefined reference to `_fft wf_malloc' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0xf4): undefined reference to `_fft wf_plan_many_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x14e): undefined reference to `_ff twf_plan_many_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x1a5): undefined reference to `_ff twf_plan_many_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x1fc): undefined reference to `_ff twf_plan_many_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x253): undefined reference to `_ff twf_plan_many_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2aa): more undefined references t o `_fftwf_plan_many_dft' follow .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3b1): undefined reference to `_ff twf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3bd): undefined reference to `_ff twf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3e7): undefined reference to `_ff twf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3ef): undefined reference to `_ff twf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x461): undefined reference to `_ff twf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x476): undefined reference to `_ff twf_destroy_plan' this continues for a long time and then I get the error at the bottom: .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined reference to `_f ftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefined references to `_fftwf_destroy_plan' follow .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined reference to `_f ftwf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined reference to `_f ftwf_free' collect2: ld returned 1 exit status Makefile:387: recipe for target `libmd.la' failed make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src/mdlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 looks like a different set of errors here. Do you think it might have to do with using FFTW-3.3? On Fri, Dec 30, 2011 at 6:30 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 31/12/2011 3:13 AM, Rashek Kazi wrote: I am currently attempting to install gromacs-4.5.5. on a winXP 32bit system through Cygwin. I had previously installed gromacs-4.5.4 without any issue but now I get an error during Make that reads like the following... Yep. See http://lists.gromacs.org/pipermail/gmx-users/2011-November/065886.htmlfor explanation and work-around for 4.5.5. Mark mv -f .deps/pthreads.Tpo .deps/pthreads.Plo /bin/sh ../../../libtool --tag=CC--mode=compile cc -DHAVE_CONFIG_H -I. -I.. /../../src -I/usr/include/libxml2 -I../../../include -I/usr/local/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-lo ops -std=gnu99 -fexcess-precision=fast -I./include -MT numa_malloc.lo -MD -MP - MF .deps/numa_malloc.Tpo -c -o numa_malloc.lo numa_malloc.c cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2 -I../../../include -I/usr/local/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unu sed -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -I./include -MT numa_malloc.lo -MD -MP -MF .deps/numa_malloc.Tpo -c numa_malloc.c -DPIC -o .li bs/numa_malloc.o
Re:[gmx-users] copper and His residues
You do not need to fix the copper in the calculation. There are must be some negative charged residues around the copper. Therefore, the copper will located at the place where it should be. regards. -- Xianqiang Sun Email: xianqi...@theochem.kth.se Division of Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology S-106 91 Stockholm, Sweden At 2012-01-04 01:15:34,ljin1988 ljin1...@126.com wrote: Hello, I am a beginner of Gromacs, and I am working with enzyme that contains two Cu2+ ions in the active site. I have found two solution to treat copper ions and surrounding His residues. First solution is adding position restrain to these ions, while the second one is defining bonds between copper ions and surrounding His residues. I just wonder about which one should I adopt? Thanks very much. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CHARMM27 Force field
Hi all, I want to know if I can implement the CHARMM27 parameter file in gromacs-4.0.7 thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] copper and His residues
xianqiang wrote: You do not need to fix the copper in the calculation. There are must be some negative charged residues around the copper. Therefore, the copper will located at the place where it should be. I agree that a position restraint on copper is not appropriate, but I strongly disagree with the assumption that it will simply be held in place by virtue of negative charges. I know of many cases where the MM approximations and electrostatic interactions were insufficient to preserve active-site geometry. There are a number of QM/MM studies that have concluded that fixed point charges on such species suffer from many limitations, not the least of which are inductive effects and the inability to account for orbital geometry. A series of distance restraints between ligating residues and the copper ion itself may be the best approach for standard MD simulations. -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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] make error Makefile:347: recipe for target `all-recursive' failed for Gromacs-4.5.5
On 4/01/2012 5:04 AM, Rashek Kazi wrote: Hi Mark (and all) Thanks for the response. I ran ./configure --disable-threads this time. ./configure went fine but again upon doing Make I have received a new error: Creating library file: .libs/libmd.dll.a .libs/fft5d.o:fft5d.c:(.text+0x140f): undefined reference to `_fftwf_plan_guru_d ft' .libs/fft5d.o:fft5d.c:(.text+0x18d1): undefined reference to `_fftwf_plan_guru_d ft_r2c' .libs/fft5d.o:fft5d.c:(.text+0x194b): undefined reference to `_fftwf_plan_guru_d ft_c2r' .libs/fft5d.o:fft5d.c:(.text+0x1aef): undefined reference to `_fftwf_execute' .libs/fft5d.o:fft5d.c:(.text+0x2133): undefined reference to `_fftwf_execute' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x4a): undefined reference to `_fft wf_malloc' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x67): undefined reference to `_fft wf_malloc' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x84): undefined reference to `_fft wf_malloc' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0xf4): undefined reference to `_fft wf_plan_many_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x14e): undefined reference to `_ff twf_plan_many_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x1a5): undefined reference to `_ff twf_plan_many_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x1fc): undefined reference to `_ff twf_plan_many_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x253): undefined reference to `_ff twf_plan_many_dft' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2aa): more undefined references t o `_fftwf_plan_many_dft' follow .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3b1): undefined reference to `_ff twf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3bd): undefined reference to `_ff twf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3e7): undefined reference to `_ff twf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3ef): undefined reference to `_ff twf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x461): undefined reference to `_ff twf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x476): undefined reference to `_ff twf_destroy_plan' this continues for a long time and then I get the error at the bottom: .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined reference to `_f ftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefined references to `_fftwf_destroy_plan' follow .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined reference to `_f ftwf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined reference to `_f ftwf_free' collect2: ld returned 1 exit status Makefile:387: recipe for target `libmd.la http://libmd.la' failed make[3]: *** [libmd.la http://libmd.la] Error 1 make[3]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src/mdlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 looks like a different set of errors here. Do you think it might have to do with using FFTW-3.3? Yes. Configure thought it found FFTW3, but now you can't link to it. See the general installation instructions for the right kind of approach. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] CHARMM27 Force field
On 4/01/2012 6:49 AM, najwa drici wrote: Hi all, I want to know if I can implement the CHARMM27 parameter file in gromacs-4.0.7 Yes, you can implement CHARMM27, but no you will not be able to use the files from GROMACS 4.5 without heavy modification. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb files using hex resid
I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Folding rate
Thanks for all your replies. I want to know this can be done in gromacs or not - using REMD with structure based models generated from SMOG server to study protein folding and unfolding ??. Also, I have a question about how to determine the exchange probablities for a particular REMD experiment and also how many replicas do we need to consider, does that depend on the temperature list generated from the T_REMD server?? On Sat, Dec 31, 2011 at 11:36 AM, felmer...@uchile.cl felmer...@uchile.clwrote: Yeah sure. There are several methods to trick your peptide to fold, but often you loose the real kinetics by using them. I think a 230 residues protein is too big to study folding kinetics through MD (because of the folding kinetics, not the size of the system). With topology based potenitials (Go-like models) you surely can do it, but take into account the the core asumption there is that the energy landscape of your peptide is perfectly funneled to the native state, which is a very good approximation for small protein (like a 100 residues) but not so nice for bigger proteins. In fact, even small proteins have intermediate states which makes the energy landscape somehow rugged (the engrailed homeodomain, the trp repressor, etc). Besides that, it is not a trivial task to go from the reduced representation to real kinetic constants. Maybe if you are interested in comparison rather than absolute values you can be lucky with the Go-modeling. If that is the case maybe you should try the SMOG potential it is very fast. regards Mensaje original De: bharat.85.m...@gmail.com Fecha: 30-dic-2011 22:45 Para: Discussion list for GROMACS usersgmx-users@gromacs.org Asunto: Re: [gmx-users] Re: Folding rate The protein that I am dealing with is a 230 amino acid protein. I have come across some methods that used reduced space model of protein such as CABS for locating the protein folding pathway. An another paper describes about using Go model together with Rigid body dynamics for finding protein folding pathway. On Sat, Dec 31, 2011 at 10:23 AM, felmer...@uchile.cl felmer...@uchile.cl wrote: I small thing to consider with that particular paper is that DE Shaw has a special machine (Anton) to do those calculations, so in principle it is not possible to reproduce them (in a reasonable amount of time) on a regular (super)computer. I think your best shot, if your protein is small enough, is to use accelerated MD mixed with some good old kramer's theory. See for example J. Chem. Theory Comput., 2011, 7 (3), pp 575–581. In any case it seems to me like too much of an effort, in the end here you really rely in the accuracy of the forcefield. Regards Mensaje original De: jmda...@itqb.unl.pt Fecha: 30-dic-2011 21:40 Para: Discussion list for GROMACS usersgmx-users@gromacs.org Asunto: Re: [gmx-users] Re: Folding rate As it was pointed out, the literature is vast on this subject. Moreover, calculating folding rates from simulations is not a trivial subject, and it relies on many assumptions (e.g. what is considered folded, that the sampling obtained is enough). Even for small peptides, enough sampling may mean several hundreds of microsseconds, something not accessible to everyone. For a very recent article on the subject, check out: Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How Fast-Folding Proteins Fold, *Science* 334:517-520. http://dx.doi.org/10.1126/science.1208351 Regards, João On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi k...@chemistry.umass.eduwrote: As Justin pointed out, there is a vast literature on this topic, you need to ask yourself what you seek, and look at many review articles to find some reasonable starting points for you own needs and designs. Beyond that, it's a lot of hard work... On Dec 30, 2011, at 7:04 PM, bharat gupta wrote: Thanks for your advice... Could you please refer me some papers regarding this On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi k...@chemistry.umass.eduwrote: No, there is no way to use such data to determine the folding rate of the intact protein. If you used a fragment approach you could potentially (read lots of papers on REMD) isolate nucleation sites, but minus the tertiary interaction scheme you could not tell a compelling story. Now, if you want to find nucleation sites and see if there are spatially proximal sites and simulate them together... You might begin to tell a story. Ken On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote: bharat gupta wrote: Thanks for your reply. I want to whether does it make any sense or is it possible to simulate fragments of proteins and find their folding rate and then correlate it to folding rate of whole protein ?? Simulating arbitrary parts of a protein may or may not produce any relevant information, likely the latter. Independently folding domains might be simulated in isolation, but if there
Re: [gmx-users] pdb files using hex resid
On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Folding rate
On 4/01/2012 12:35 PM, bharat gupta wrote: Thanks for all your replies. I want to know this can be done in gromacs or not - using REMD with structure based models generated from SMOG server to study protein folding and unfolding ??. Well, it can be done, but you probably don't have enough computer to fold a 230 residue protein at atomistic resolution (or maybe even coarse-grained). Also, I have a question about how to determine the exchange probablities for a particular REMD experiment and also how many replicas do we need to consider, does that depend on the temperature list generated from the T_REMD server?? There's a significant literature on these subjects. I suggest you read some of it. Short answer: pick the highest temperature according to the size of the largest barrier you expect to cross (good luck guessing that), have around 20% exchange acceptance, and be prepared to observe where the replica-flow bottle necks are and to iteratively refine you temperatures. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Folding rate
Thanks for the reply. Since I need to study the effect of beta-hairpin turn design on protein folding . I thought that first unfolding and then refolding would give the change in folding time. As you told that to do such a task would require large computational power. Is there any other method in MDS that could be used ?? On Wed, Jan 4, 2012 at 10:52 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/01/2012 12:35 PM, bharat gupta wrote: Thanks for all your replies. I want to know this can be done in gromacs or not - using REMD with structure based models generated from SMOG server to study protein folding and unfolding ??. Well, it can be done, but you probably don't have enough computer to fold a 230 residue protein at atomistic resolution (or maybe even coarse-grained). Also, I have a question about how to determine the exchange probablities for a particular REMD experiment and also how many replicas do we need to consider, does that depend on the temperature list generated from the T_REMD server?? There's a significant literature on these subjects. I suggest you read some of it. Short answer: pick the highest temperature according to the size of the largest barrier you expect to cross (good luck guessing that), have around 20% exchange acceptance, and be prepared to observe where the replica-flow bottle necks are and to iteratively refine you temperatures. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb files using hex resid
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers ? I thought the resid field was fixed at 4 digits... If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Is there a configure flag that controls this? and do you mean dlpolyplugin.so ? Is there another tool with which I can do specific selections and write them out to something I can reinput into gromacs? -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb files using hex resid
On 4/01/2012 1:07 PM, Peter C. Lai wrote: On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers ? I thought the resid field was fixed at 4 digits... Correct, it doesn't. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Yes, you just make the path with your installed VMD libraries available in the linking path, just like with FFTW or whatever. Is there a configure flag that controls this? Yes. It's enabled by default, but there is no attempt to check that a VMD installation exists. and do you mean dlpolyplugin.so ? No. DLPOLY is a MDS program, IIRC. Is there another tool with which I can do specific selections and write them out to something I can reinput into gromacs? Script g_select? 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Folding rate
Actually i know people using Go-models to study protein folding for proteins as large as 300 aa. Now, in these cases you need to use biasing potentials and not temperature exchages (maybe both?). In principle, the REMD will help you with the comformational exchange but it also includes a new level of complexity since the temperature distribution for the correct exchange ratios is pretty much an empiric issue. In principle, there is no problem to run these simulations independently and then combining them by WHAM taking the temperature as the only bias. Just consider the parallel tempering as a sampling enhancer the same way as it is used also with hamiltonian hopping. If you go for the umbrella sampling way you can use the PLUMED plugin for colective variables. There you can apply a bias directly to the number of contacts of the structure (a contact map bias) or maybe to the gyration radius. In principle, once you unbias your histograms you can calculate the free energy profile of any colective variable using a multidimensional histogram trick. In the end, what you need to now is how much energy you are adding to sample that state. Once you have the free energy profile at the folding temperature (this also needs some trial and error) you should be able to measure the height of the energetic barrier between states which is in principle what determines that transition rates. As mark said, there are tons of papers of this as Go-models ar practically the only way people had to explore the protein folding thermodynamics in the computer. regards Felipe Mensaje originalDe: mark.abra...@anu.edu.auFecha: 03-ene-2012 22:52Para: Discussion list for GROMACS usersgmx-users@gromacs.orgAsunto: Re: [gmx-users] Re: Folding rateOn 4/01/2012 12:35 PM, bharat gupta wrote: Thanks for all your replies. I want to know this can be done in gromacs or not - using REMD with structure based models generated from SMOG server to study protein folding and unfolding ??.Well, it can be done, but you probably don't have enough computer to fold a 230 residue protein at atomistic resolution (or maybe even coarse-grained). Also, I have a question about how to determine the exchange probablities for a particular REMD experiment and also how many replicas do we need to consider, does that depend on the temperature list generated from the T_REMD server??There's a significant literature on these subjects. I suggest you read some of it. Short answer: pick the highest temperature according to the size of the largest barrier you expect to cross (good luck guessing that), have around 20% exchange acceptance, and be prepared to observe where the replica-flow bottle necks are and to iteratively refine you temperatures.Mark-- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-usersPlease search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem with checking performance
Hello: I submit MD jobs to cluster with the following scrips: # @ job_name = gromacs_job # @ class = kdm-large # @ account_no = G07-13 # @ error = gromacs.out # @ output = gromacs.out # @ environment = COPY_ALL # @ wall_clock_limit = 2:00:00 # @ notification = error # @ notify_user = alb...@icm.edu.pl # @ job_type = bluegene # @ bg_size = 128 # @ queue mpirun -exe /opt/gromacs/4.5.4/bin/mdrun_mpi -args -nosum -dlb yes -s nvt -mode VN -np 128 and it generate the following files; gromacs.out md.log traj.trr ener.edr I check the tail of each file and cannot find the performance of my job, such as: how long it will take to be finished. Does anybody have any idea to fix this? THX -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with checking performance
Albert wrote: Hello: I submit MD jobs to cluster with the following scrips: # @ job_name = gromacs_job # @ class = kdm-large # @ account_no = G07-13 # @ error = gromacs.out # @ output = gromacs.out # @ environment = COPY_ALL # @ wall_clock_limit = 2:00:00 # @ notification = error # @ notify_user = alb...@icm.edu.pl # @ job_type = bluegene # @ bg_size = 128 # @ queue mpirun -exe /opt/gromacs/4.5.4/bin/mdrun_mpi -args -nosum -dlb yes -s nvt -mode VN -np 128 and it generate the following files; gromacs.out md.log traj.trr ener.edr I check the tail of each file and cannot find the performance of my job, such as: how long it will take to be finished. Does anybody have any idea to fix this? mdrun -v prints a running estimate of job completion time, otherwise there is no indication of performance until the job is over and final statistics are printed to the end of the .log 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb files using hex resid
On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote: On 4/01/2012 1:07 PM, Peter C. Lai wrote: On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers ? I thought the resid field was fixed at 4 digits... Correct, it doesn't. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Yes, you just make the path with your installed VMD libraries available in the linking path, just like with FFTW or whatever. Is there a configure flag that controls this? Yes. It's enabled by default, but there is no attempt to check that a VMD installation exists. and do you mean dlpolyplugin.so ? No. DLPOLY is a MDS program, IIRC. No dlopen.so in the molfile plugin lib directory. Perhaps things have changed between VMD 1.8 and 1.9 Is there another tool with which I can do specific selections and write them out to something I can reinput into gromacs? Script g_select? That sounds good. Although I may have a workaround by altering my procedure. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb files using hex resid
On 4/01/2012 2:19 PM, Peter C. Lai wrote: On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote: On 4/01/2012 1:07 PM, Peter C. Lai wrote: On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers ? I thought the resid field was fixed at 4 digits... Correct, it doesn't. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Yes, you just make the path with your installed VMD libraries available in the linking path, just like with FFTW or whatever. Is there a configure flag that controls this? Yes. It's enabled by default, but there is no attempt to check that a VMD installation exists. and do you mean dlpolyplugin.so ? No. DLPOLY is a MDS program, IIRC. No dlopen.so in the molfile plugin lib directory. Perhaps things have changed between VMD 1.8 and 1.9 Sorry, dlopen is the mechanism that allows the executing code to see if a dynamic link library contains a function that delivers the required functionality. So it's just a matter of having the VMD stuff in the dynamic linking path. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb files using hex resid
On 2012-01-04 02:54:28PM +1100, Mark Abraham wrote: On 4/01/2012 2:19 PM, Peter C. Lai wrote: On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote: On 4/01/2012 1:07 PM, Peter C. Lai wrote: On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers ? I thought the resid field was fixed at 4 digits... Correct, it doesn't. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Yes, you just make the path with your installed VMD libraries available in the linking path, just like with FFTW or whatever. Is there a configure flag that controls this? Yes. It's enabled by default, but there is no attempt to check that a VMD installation exists. and do you mean dlpolyplugin.so ? No. DLPOLY is a MDS program, IIRC. No dlopen.so in the molfile plugin lib directory. Perhaps things have changed between VMD 1.8 and 1.9 Sorry, dlopen is the mechanism that allows the executing code to see if a dynamic link library contains a function that delivers the required functionality. So it's just a matter of having the VMD stuff in the dynamic linking path. Well I added -I/usr/local/vmd/plugins/include to CPPFLAGS and -L/usr/local/vmd/plugins/FREEBSDAMD64/molfile to LDFLAGS and the recompiled editconf is still uable to properly parse the vmd-style pdb Oh well -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb files using hex resid
On 4/01/2012 2:59 PM, Peter C. Lai wrote: On 2012-01-04 02:54:28PM +1100, Mark Abraham wrote: On 4/01/2012 2:19 PM, Peter C. Lai wrote: On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote: On 4/01/2012 1:07 PM, Peter C. Lai wrote: On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote: On 4/01/2012 12:30 PM, Peter C. Lai wrote: I used VMD to process a gro file and wrote it to pdb, because VMD can't write gro files. Because the # of residues exceeds , it numbered the remaining residues in the PDB in 4 bit hex. Editconf will not convert the hex numbered residue ids back to decimal (it just truncates anything past the final 0-9 digit in the field). Does this mean if I feed the pdb as-is into grompp it will also have problems reading the residue numbers? Gromacs 4.5.3 Yes. VMD is writing non-standard-compliant PDB. Blame it. Does the PDB format even support residue numbers? I thought the resid field was fixed at 4 digits... Correct, it doesn't. If you've linked GROMACS to the dlopen library from VMD (the default) then GROMACS can read whatever VMD writes, so pick a useful format. Can you elaborate on this? Yes, you just make the path with your installed VMD libraries available in the linking path, just like with FFTW or whatever. Is there a configure flag that controls this? Yes. It's enabled by default, but there is no attempt to check that a VMD installation exists. and do you mean dlpolyplugin.so ? No. DLPOLY is a MDS program, IIRC. No dlopen.so in the molfile plugin lib directory. Perhaps things have changed between VMD 1.8 and 1.9 Sorry, dlopen is the mechanism that allows the executing code to see if a dynamic link library contains a function that delivers the required functionality. So it's just a matter of having the VMD stuff in the dynamic linking path. Well I added -I/usr/local/vmd/plugins/include to CPPFLAGS and -L/usr/local/vmd/plugins/FREEBSDAMD64/molfile to LDFLAGS and the recompiled editconf is still uable to properly parse the vmd-style pdb Sure... presumably the VMD stuff is only invoked for file types for which there is not native support. Note that I suggested using some other intermediate format, not trying to read the non-standard PDB. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] forcefield.itp file for gromos45a3 and oplsaa
Hello I am trying to adjust compound LJ parameter in oplsaa (sigmaepsilon) and also in Gromos (C6 and C12) forcefield for comparison. The original ffnonbonded.itp file in oplsaa.ff has no pair potential listed. While the original ffnonbonded.itp file in gromos**.ff listed all the pair potentials. If I change one atom potential, do I need to do anything to generate the new pair potential before running a simulation in opls-aa force field? Or how to generate the pair potentials? While for the case of gromos forcefield, the forcefield.itp file shows no pair potential will be generated. Is there any automatic ways to generate the modified LJ potentials? Should I list every possible LJ pair potentials in nonbonded.itp file? It looks like some very tedious work if several atoms are going to be modified. Also, what does fudge LJ and fudgeQQ mean in forcefield.itp file? Values of those two are different for OPLS and Gromos. Thanks in advance and happy new year! Best! Xueming -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] forcefield.itp file for gromos45a3 and oplsaa
On 4/01/2012 4:43 PM, XUEMING TANG wrote: Hello I am trying to adjust compound LJ parameter in oplsaa (sigmaepsilon) and also in Gromos (C6 and C12) forcefield for comparison. The original ffnonbonded.itp file in oplsaa.ff has no pair potential listed. While the original ffnonbonded.itp file in gromos**.ff listed all the pair potentials. If I change one atom potential, do I need to do anything to generate the new pair potential before running a simulation in opls-aa force field? Or how to generate the pair potentials? While for the case of gromos forcefield, the forcefield.itp file shows no pair potential will be generated. Is there any automatic ways to generate the modified LJ potentials? Should I list every possible LJ pair potentials in nonbonded.itp file? It looks like some very tedious work if several atoms are going to be modified. Also, what does fudge LJ and fudgeQQ mean in forcefield.itp file? Values of those two are different for OPLS and Gromos. In general, two force fields work differently and have their own idiosyncrasies that will show up in how GROMACS implements them. When modifying them, you should be sure to check the original literature and the GROMACS manual and satisfy yourself how your changes will work. You should search the manual for discussion of the use of gen-pairs and the fudge values. I don't know why the list of [ nonbond_param ] values is exhaustive - you'd think the combination rules could be used. In practice, you only need to add parameters for interactions that can occur in your system, and grompp will complain about those that it can't find. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Help with non-standard residues and molecular structures
I'd appreciate any help -- I'm trying to model a small (~ 20-carbon ) molecule linked to a diamond surface. I got the diamond surface with 1500 atoms working fine all the way through to the MD simulation and it looks great. But I'm getting stuck on the molecule, which is not a protein but a moderately short-chain molecule that has a triazole (N3C2) in the middle of it. I thought in order to make this work I would need ot learn how to with non-standard residues and after reading through the manual endless times and searching on the web site and trying things I'm basically stuck. I thought it would easiest to deal with the triazole ring by creating it as a non-standard residue in aminoacids.n2t. As a starting point I thought I would try to work slowly by modifying an existing residue, so I arbitrary decided to modify alanine in order to understand how to work toward the more complicated triazole ring. So, in atomtypebyname.atp I copied the entry for ALA and called it ZZZ, and added a new entry ZZZ Protein into residuetypes.dat. At that point I can read in a pdb file with atoms belonging to residue ZZZ and pdb2gmx works fine. However, if I try to change one of the carbon atoms to a nitrogen, (say, chance CA to N or NA), I get errors (see below) that I'm having trouble interpreting. I thought that perhaps it was a problem of having two atoms with the same definition, so I made one N1 and one N2 as below, and also tried other variations (e.g., NA1 and NA2) (This is my entry in aminoacids.n2t) [ ZZZ ] [ atoms ] N1opls_238 -0.500 1 Hopls_2410.300 1 N2 opls_238 0.140 1 HAopls_1400.060 1 CBopls_135 -0.180 2 HB1opls_1400.060 2 HB2opls_1400.060 2 HB3opls_1400.060 2 Copls_2350.500 3 Oopls_236 -0.500 3 [ bonds ] N1 H N1N2 N2HA N2CB N2 C CB HB1 CB HB2 CB HB3 C O -C N1 [ impropers ] -CN2 N1 Himproper_Z_N_X_Y N2+N1 C Oimproper_O_C_X_Y I thought that this would lead to a structure that would connect C to the previous residue in my pdb file and the N to the next . However, when I do pdb2gmx, I get: ** Back Off! I just backed up topol.top to ./#topol.top.40# Processing chain 1 (13 atoms, 1 residues) There are 0 donors and 1 acceptors There are 0 hydrogen bonds Identified residue ZZZ1 as a starting terminus. Identified residue ZZZ1 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Start terminus ZZZ-1: NH3+ End terminus ZZZ-1: COO- --- Program pdb2gmx, VERSION 4.5.3 Source code file: /build/buildd/gromacs-4.5.3/src/kernel/pdb2top.c, line: 1056 Fatal error: atom N not found in buiding block 1ZZZ while combining tdb and rtp I'm using the oplsaa force field, but up to this point it was a pretty arbitrary decision. I think my problem is understanding the mapping between atom names ( N1, HB1, etc) and the opls names, as I haven't yet found a good explanation for how this mapping is done and/or what flexibility one has in creating atom names for non-standard residues. (So, am I allowed to create a N atom and call it N1, as long as I assign it to an existing opls_xxx number ?) . Any suggestions would be very welcome Thanks! Bob Hamers -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
