[gmx-users] G_hbond and periodicity
Hi all, Does periodic boundary affect the calculation of hydrogen bond if my protein is not in one box? What about other calculations? Thank you, Tang jiaowei ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ffamber updates
Hi Eric Thanks for doing that great job concerning the amberFF for GROMACS. I recently came across this paper: http://www.biophysj.org/cgi/content/abstract/92/11/3817?maxtoshow=HITS=10hits=10RESULTFORMAT=searchid=1FIRSTINDEX=0volume=92firstpage=3817resourcetype=HWCIT There Perez et al refined new alpha/gamma angles for nucleic acids. They claim, that these dihedrals in the original amber99 lead to irreversible transitions, which have an influence on the correct conformation of NA-strands. I thought about including them in the amber99-GROMACS port, but maybe it's better if you do, because you have more experience in building the amber-ports. What do you think? I didn't read the paper according to your 99sb-port yet. Do you think it makes sense to switch from the amber99 to amber99sb? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Eric J. Sorin wrote: Hi GROMACS users, We've updated our ffamber ports to include the AMBER-99SB force field. Please visit the new website for information and downloads: http://chemistry.csulb.edu/ffamber/. Eric ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] fatal error in nsgrid
I've been running on 16 processors a protein MD simulation. During the simulation I've got a crash and the standard error reported this: Fatal error: ci = 10280 should be in 0 .. 10050 [FILE nsgrid.c, LINE 218] [0] MPI Abort by user Aborting program ! [0] Aborting program! What could that be? Fabio ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] G_hbond and periodicity
Hi Tang Jiaowei, g_hbond takes periodicity into account, like most tools do. Do note that this doesn't work if you've performed rotational transformations (lsq-fitting). Cheers, Tsjerk On 9/28/07, tangxuan [EMAIL PROTECTED] wrote: Hi all, Does periodic boundary affect the calculation of hydrogen bond if my protein is not in one box? What about other calculations? Thank you, Tang jiaowei ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs result
Right, but I can just warn anyone. Trying to use TI on a docked structure is insanity... The docked structure is an approximation in its best case (more likely its simply crap). Applying a free energy calculation towards such a structure will give you everything...but sure not the the correct free energy of bindingexcept you are very luckyIF you are that lucky, play lottery instead and enjoy life ;) In fact it's (citating Mark) another expensive random number generator... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Mark Abraham wrote: mahbubeh zarrabi wrote: Dear all I have 3 complexes of docking.(one receptor with 3 different ligands).I studied MD of 3 complexes in 15 ns by gromacs.how can i compare binding energy and affinity of 3 ligands with receptor.(how can i analysis gromacs result) Shouldn't you have asked this question before designing your simulations? :-) You can't measure binding affinity without taking a difference between before and after, which you don't seem to have. You probably need to look at literature on thermodynamic integration, or some such. 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs result
Maik Goette wrote: Right, but I can just warn anyone. Trying to use TI on a docked structure is insanity... The docked structure is an approximation in its best case (more likely its simply crap). Applying a free energy calculation towards such a structure will give you everything...but sure not the the correct free energy of bindingexcept you are very luckyIF you are that lucky, play lottery instead and enjoy life ;) In fact it's (citating Mark) another expensive random number generator... I think you're exaggerating a bit. Docking works quite well if you do it correctly, that is many (=100) tries. See my website below for some useful publications on docking... -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, 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 [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ffamber updates
Hi Maik, These updated NA params would be nice to add and test, but I've been too busy lately to do this. I'd like to get to it soon though (i.e. this year ;o) As for AMBER-99SB, the paper makes reasonable arguments I think, but I've not run any real test or production runs with 99SB myself, so I can't comment on it w.r.t. any specific systems. Eric - Original Message - From: Maik Goette [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org; [EMAIL PROTECTED] Sent: Friday, September 28, 2007 2:57 AM Subject: Re: [gmx-users] ffamber updates Hi Eric Thanks for doing that great job concerning the amberFF for GROMACS. I recently came across this paper: http://www.biophysj.org/cgi/content/abstract/92/11/3817?maxtoshow=HITS=10hits=10RESULTFORMAT=searchid=1FIRSTINDEX=0volume=92firstpage=3817resourcetype=HWCIT There Perez et al refined new alpha/gamma angles for nucleic acids. They claim, that these dihedrals in the original amber99 lead to irreversible transitions, which have an influence on the correct conformation of NA-strands. I thought about including them in the amber99-GROMACS port, but maybe it's better if you do, because you have more experience in building the amber-ports. What do you think? I didn't read the paper according to your 99sb-port yet. Do you think it makes sense to switch from the amber99 to amber99sb? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Eric J. Sorin wrote: Hi GROMACS users, We've updated our ffamber ports to include the AMBER-99SB force field. Please visit the new website for information and downloads: http://chemistry.csulb.edu/ffamber/. Eric ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Reading XTC files from fortran90
Hi all. I'm writing this beucase I'm having terrible problems in trying to deal with gromacs trajectory files with my own programs, originally written on fortran90. The codes themselves are enoughly big to make it out of question to try to translate them. What leads to some sort of mixed language compilation. My first guess was to try to use the guidelines from http://xray.bmc.uu.se/~spoel/md/online/xtc.html, but it absolutelly didn't worked. Could not find a compatible library. Tried to recompile gromacs in order to do so, but instead of a libsdrf.a library file, it created just common .lo and .o object files. Looked inside concoord program, as there are some mentions in the list to look at the code. Was a really good aprentize, could understand better the logics involved when dealing with .xtc files, BUT I could not use the library files that came with that. Somehow, it wasn't recognized as a valid file. My last try up to now was to try to link my test-read-program with the libxdrf object file. It yelded the following error: CruNumMac src/own/B/9/xtc 238% ifort libxdrf.lo xtciof.f90 test_xtc.f90 IPO: WARNING: no IR in object file libxdrf.lo; was the source file compiled with -ipo? IPO Error: unresolved : xdrfint_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrfclose_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrfopen_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrffloat_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrf3dfcoord_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO: performing multi-file optimizations IPO: generating object file /tmp/ipo_ifortZNvZHh.o test_xtc.f90(17) : (col. 3) remark: LOOP WAS VECTORIZED. test_xtc.f90(25) : (col. 8) remark: LOOP WAS VECTORIZED. xtciof.f90(112) : (col. 3) remark: LOOP WAS VECTORIZED. libxdrf.lo: file not recognized: File format not recognized If I try to link to the .o objetc: CruNumMac src/own/B/9/xtc 240% ifort libxdrf.o xtciof.f90 test_xtc.f90 IPO: WARNING: no IR in object file libxdrf.o; was the source file compiled with -ipo? IPO Error: unresolved : xdrfint_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrfclose_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrfopen_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrffloat_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrf3dfcoord_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : ffclose Referenced in libxdrf.o IPO: performing multi-file optimizations IPO: generating object file /tmp/ipo_ifort2f5KMw.o test_xtc.f90(17) : (col. 3) remark: LOOP WAS VECTORIZED. test_xtc.f90(25) : (col. 8) remark: LOOP WAS VECTORIZED. xtciof.f90(112) : (col. 3) remark: LOOP WAS VECTORIZED. /tmp/ipo_ifort2f5KMw.o(.text+0x1e1): In function `MAIN__': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x4ea):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfclose_' /tmp/ipo_ifort2f5KMw.o(.text+0x517):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x92b): In function `xtciof_mp_xtcheader_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x941):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x95e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x97b):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xb8e): In function `xtciof_mp_xtcio_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xbde):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xc2e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xc7e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xcce):/tmp/ipo_ifort2f5KMw.f: more undefined references to `xdrffloat_' follow /tmp/ipo_ifort2f5KMw.o(.text+0xe6b): In function `xtciof_mp_xtcio_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrf3dfcoord_' /tmp/ipo_ifort2f5KMw.o(.text+0xfc6): In function `xtciof_mp_xtcopen_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x1292):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfclose_' /tmp/ipo_ifort2f5KMw.o(.text+0x12b3):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x134e): In function `xtciof_mp_xtccoord_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0x139f):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0x13f0):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0x1441):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_'
Re: [gmx-users] Reading XTC files from fortran90
Hi, try: download http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz (and optionally issue a 'make' in the xtc directory after unpacking) in the linking stage, use something like ifort -blabla -lxdrf -L/wherever/xtc -lg2c your smalll test code looks OK apart from the fact that I don't know what happens if you readwrite from the same file. Bert On Sat, 29 Sep 2007, Jones de Andrade wrote: Hi all. I'm writing this beucase I'm having terrible problems in trying to deal with gromacs trajectory files with my own programs, originally written on fortran90. The codes themselves are enoughly big to make it out of question to try to translate them. What leads to some sort of mixed language compilation. My first guess was to try to use the guidelines from http://xray.bmc.uu.se/~spoel/md/online/xtc.html, but it absolutelly didn't worked. Could not find a compatible library. Tried to recompile gromacs in order to do so, but instead of a libsdrf.a library file, it created just common .lo and .o object files. Looked inside concoord program, as there are some mentions in the list to look at the code. Was a really good aprentize, could understand better the logics involved when dealing with .xtc files, BUT I could not use the library files that came with that. Somehow, it wasn't recognized as a valid file. My last try up to now was to try to link my test-read-program with the libxdrf object file. It yelded the following error: CruNumMac src/own/B/9/xtc 238% ifort libxdrf.lo xtciof.f90 test_xtc.f90 IPO: WARNING: no IR in object file libxdrf.lo; was the source file compiled with -ipo? IPO Error: unresolved : xdrfint_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrfclose_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrfopen_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrffloat_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrf3dfcoord_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO: performing multi-file optimizations IPO: generating object file /tmp/ipo_ifortZNvZHh.o test_xtc.f90(17) : (col. 3) remark: LOOP WAS VECTORIZED. test_xtc.f90(25) : (col. 8) remark: LOOP WAS VECTORIZED. xtciof.f90(112) : (col. 3) remark: LOOP WAS VECTORIZED. libxdrf.lo: file not recognized: File format not recognized If I try to link to the .o objetc: CruNumMac src/own/B/9/xtc 240% ifort libxdrf.o xtciof.f90 test_xtc.f90 IPO: WARNING: no IR in object file libxdrf.o; was the source file compiled with -ipo? IPO Error: unresolved : xdrfint_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrfclose_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrfopen_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrffloat_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrf3dfcoord_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : ffclose Referenced in libxdrf.o IPO: performing multi-file optimizations IPO: generating object file /tmp/ipo_ifort2f5KMw.o test_xtc.f90(17) : (col. 3) remark: LOOP WAS VECTORIZED. test_xtc.f90(25) : (col. 8) remark: LOOP WAS VECTORIZED. xtciof.f90(112) : (col. 3) remark: LOOP WAS VECTORIZED. /tmp/ipo_ifort2f5KMw.o(.text+0x1e1): In function `MAIN__': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x4ea):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfclose_' /tmp/ipo_ifort2f5KMw.o(.text+0x517):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x92b): In function `xtciof_mp_xtcheader_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x941):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x95e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x97b):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xb8e): In function `xtciof_mp_xtcio_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xbde):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xc2e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xc7e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xcce):/tmp/ipo_ifort2f5KMw.f: more undefined references to `xdrffloat_' follow /tmp/ipo_ifort2f5KMw.o(.text+0xe6b): In function `xtciof_mp_xtcio_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrf3dfcoord_' /tmp/ipo_ifort2f5KMw.o(.text+0xfc6): In function `xtciof_mp_xtcopen_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x1292):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfclose_'
