[gmx-users] Postdoctoral and staff scientist positions in the Gromacs teams
Hi! As we have occasionally done in the past on this list, I just want to mention that we currently have a couple of openings in the Gromacs team in Stockholm if you're interested (or know somebody who might be). Subject: Postdoctoral staff scientist positions: Development of Next-Generation Parallel Algorithms for Molecular Dynamics We are looking for exceptionally talented researchers interested in inventing the next-generation parallel algorithms for molecular simulation, mostly related to GROMACS. Potential projects include: * Techniques for domain decomposition over millions of cores * Heterogeneous parallelization utilizing both CPUs and GPUs * Multi-level parallelization: threads, MPI, task parallelism * Multi-grid and multipole methods for long-range electrostatics * Markov State Models for ensemble distributed computing * Large-scale simulations of Membrane proteins and drug design We have a longer PDF ad prospect that I'd be happy to send to anyone interested! We provide a leading international research environment, competitive salaries, and the work is carried out in collaboration with partners such as the Barcelona Supercomputing Center, Oak Ridge National Labs, and RIKEN in Kobe where we have access to some of the world’s fastest supercomputers. Submit a PDF application with a CV, description of interests, and a list of publications for postdoctoral positions to Erik Lindahl e...@kth.se or Berk Hess h...@kth.se; we are also happy to answer any questions! Cheers, Erik -- Erik Lindahl e...@kth.se Professor of Theoretical Computational Biophysics, KTH Royal Institute of Technology Professor of Computational Structural Biology, Stockholm University Albanova University Center, SE-10691 Stockholm, Sweden Tel (KTH): +46 8 55378029 Tel (SU): +46 8 164675 Swedish cell: +46 73 4618050 US cell: +1 206 457 7887 -- 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: Looking for potential phosphate binding sites
bharat gupta wrote: Hi, Hi, I have done a simulation of 10ns with my proteins and 0.5 M phosphate ion. Now I want to know where does the phosphate ion bind on the protein surface or distribution of phosphate ions on protein surface ?? .. can help me finding out this Have you watched the trajectory to see what happens? -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] Partial atomic charge
parto haghighi wrote: Dear GMX users, I could make topology file of a ligand molecule by PRODRG but it has wrong charge on each atom and as mentioned in Gromacs tutorial (protein-ligand complex) I have used quantum mechanic calculation (like spartan) to correct its charge: .itp file from PRODRG: [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 10.092 15.0350 2 CH2 1 DRG CAI 10.107 14.0270 3 NL 1 DRG N 10.702 14.0067 4 H 1 DRG H 1 -0.007 1.0080 5 CH2 1 DRG CAJ 10.106 14.0270 6 CH3 1 DRG CAB 20.071 15.0350 7 CH2 1 DRG CA 20.089 14.0270 8 C 1 DRG C 20.343 12.0110 9 O 1 DRG O 2 -0.733 15.9994 10 N 1 DRG NAL 20.120 14.0067 11 H 1 DRG HKL 2 -0.009 1.0080 12 C 1 DRG CAP 20.119 12.0110 13 C 1 DRG CAN 3 -0.037 12.0110 14 CH3 1 DRG CAC 30.047 15.0350 15 CR1 1 DRG CAG 3 -0.020 12.0110 16 HC 1 DRG HAN 30.013 1.0080 17 CR1 1 DRG CAF 3 -0.020 12.0110 18HC 1 DRG HAM30.013 1.0080 19 CR1 1 DRG CAH 3 -0.020 12.0110 20 HC 1 DRG HAO 30.013 1.0080 21 C 1 DRG CAO 3 -0.036 12.0110 22 CH3 1 DRG CAD 30.047 15.0350 .itp file whit modification based on Hatree-Fock quantum chemical calculations using 6-31* basis set: ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 1-0.50715.0350 2 CH2 1 DRG CAI 10.117 14.0270 3 NL 1 DRG N 10.37214.0067 4 H 1 DRG H 10.391 1.0080 5 CH2 1 DRG CAJ 10.10414.0270 6 CH3 1 DRG CAB 2-0.512 15.0350 7 CH2 1 DRGCA 2-0.368 14.0270 8 C 1 DRG C 20.983 12.0110 9 O 1 DRG O 2-0.656 15.9994 10 N 1 DRG NAL 2-0.689 14.0067 11 H 1 DRG HKL 20.391 1.0080 12 C 1 DRG CAP 2-0.105 12.0110 13 C 1 DRG CAN 3 0.367 12.0110 14 CH3 1 DRG CAC 3-0.70015.0350 15 CR1 1 DRG CAG 3 -0.36412.0110 16 HC 1 DRG HAN 30.189 1.0080 17 CR1 1 DRG CAF 3 -0.07912.0110 18 HC 1 DRG HAM 30.1591.0080 19CR1 1 DRG CAH 3 -0.412 12.0110 20 HC 1 DRG HAO 30.2021.0080 21 C 1 DRG CAO 3 0.425 12.0110 22 CH3 1 DRG CAD 3-0.739 15.0350 .itp file of a reference (dynamic and structural properties of lidocaine in lipid bilayer,Carl-Johan Högberg, Arnold Maliniak, Alexander P. Lyubartsev ⁎ http://www.elsevier.com/locate/biophyschem ): [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CAA 10.02515.0350 2 CH2 1 DRG CAI 10.24814.0270 3 NL 1 DRG N 10.04914.0067 4 H 1 DRG H 10.405 1.0080 5 CH2 1 DRG CAJ 10.24814.0270 6 CH3 1 DRG CAB 20.02515.0350 7 CH2 1 DRG CA 20.00014.0270 8 C 1 DRG C 20.22712.0110 9 O 1 DRG O 2 -0.41115.9994 10 N 1 DRG NAL 20.08814.0067 11 H 1 DRG HKL 2 0.0081.0080 12 C 1 DRG CAP 20.088 12.0110 13 C 1 DRG CAN 3 -0.004 12.0110 14 CH3 1 DRG CAC 30.030 15.0350 15 CR1 1 DRG CAG3 -0.013 12.0110 16HC 1 DRG HAN 3 1.0080 17 CR1 1 DRG CAF 3 -0.013 12.0110 18 HC 1 DRG HAM 3 1.0080 19 CR1 1 DRG CAH 3 -0.013 12.0110 20 HC 1 DRG HAO 3 1.0080 21 C 1 DRG
[gmx-users] Re: couple-moltype of FEP
Please keep the discussion on the gmx-users list. Chunxia Gao wrote: Dear Justin, If I apply the pull code to the distance restraints, can I calculate the free energy of those restraints through g_bar? In what way? The pull code and free energy code are independent. I see no reason why you could not proceed in the same manner as the free energy tutorial describes, but with the addition of your restraint. and the pull code can only be applied to distance restraints, right? not angle or dihedral restraints? Correct. -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] Re: Looking for potential phosphate binding sites
Yes, the phosphate ion moves around the protein but I am not able to find out how many of them bind to my protein. How can that be done ?? On Thu, Dec 1, 2011 at 8:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Hi, Hi, I have done a simulation of 10ns with my proteins and 0.5 M phosphate ion. Now I want to know where does the phosphate ion bind on the protein surface or distribution of phosphate ions on protein surface ?? .. can help me finding out this Have you watched the trajectory to see what happens? -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] Re: Looking for potential phosphate binding sites
bharat gupta wrote: Yes, the phosphate ion moves around the protein but I am not able to find out how many of them bind to my protein. How can that be done ?? You'll have to set a definition for what you consider to be binding. Is a transient contact binding? Does the interaction have to persist for some length of time to be considered? In any case, you can print a list of contacts that occur with g_dist -dist, or use more complex selection criteria and generate dynamic indices with g_select (see the help text for examples). -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] Re: Looking for potential phosphate binding sites
Hi, Is there any way to get the averaged distributions of ions around the protein surface. On Thu, Dec 1, 2011 at 9:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Yes, the phosphate ion moves around the protein but I am not able to find out how many of them bind to my protein. How can that be done ?? You'll have to set a definition for what you consider to be binding. Is a transient contact binding? Does the interaction have to persist for some length of time to be considered? In any case, you can print a list of contacts that occur with g_dist -dist, or use more complex selection criteria and generate dynamic indices with g_select (see the help text for examples). -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] Re: Looking for potential phosphate binding sites
bharat gupta wrote: Hi, Is there any way to get the averaged distributions of ions around the protein surface. Start with Chapter 7 of the manual to see what's possible, then proceed to the relevant sections of Appendix D. My suspicion is that the answer to your question is not likely and certainly not directly. You may be able to combine various tools (g_mdmat, g_dist, g_rdf, etc) to produce something useful. -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] how can i merge several trajectory files to one?
Dear Experts, I am wondering it is possible to merge several trajectory pieces to one ? If it is, how can I ? Best, Hyun. -- 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] how can i merge several trajectory files to one?
Hyunsik wrote: Dear Experts, I am wondering it is possible to merge several trajectory pieces to one ? trjcat -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] how can i merge several trajectory files to one?
Thank you very much. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Thursday, December 01, 2011 11:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] how can i merge several trajectory files to one? Hyunsik wrote: Dear Experts, I am wondering it is possible to merge several trajectory pieces to one ? trjcat -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 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] compiling with the PGI compiler
Hi,
I've personally never heard of anybody using gromacs compiled with PGI.
I am using a new cluster of Xeons and, to get the most efficient
compilation, I have compiled gromacs-4.5.4 separately with the intel,
pathscale, and pgi compilers.
I did try Pathscale a few months ago and AFAIR it wasn't very
difficult to get it working - although I do remember getting some
segfaults from time to time. The Intel Compiler support in CMake is
kind of broken in 4.5, you need to fiddle with the flags a bit, but it
should be quite straightforward.
With the pgi compiler, I am most concerned about this floating point
overflow warning:
...
[ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o
[ 19%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o
[ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o
PGC-W-0129-Floating point overflow. Check constants and constant expressions
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/gmxlib/trajana/nbsearch.c:
166)
That looks like a bug, in case of real==float HUGE_VALF should be used
instead of HUGE_VAL.
PGC/x86-64 Linux 11.8-0: compilation completed with warnings
[ 19%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o
[ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o
...
There are also a lot of warnings about a type cast, which seems less like a
real problem:
Looks like all of them are enum to string-related stuff, they are harmless.
I compiled like this:
module purge
module load pgi64/11.8 openmpi_pgi64/1.4.3_ofed
module load cmake/2.8.5
export CCDIR=/opt/pgi/linux86-64/11.8/bin
## set the location of the single precision FFTW isntallation
export FFTW_LOCATION=/home/nealechr/exe/pgi/fftw-3.1.2/exec
# Nothing below this line usually needs to be changed
export CXX=pgCC
export CC=pgcc
cmake ../source/ \
-DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include \
-DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a \
-DCMAKE_INSTALL_PREFIX=$(pwd) \
-DGMX_X11=OFF \
-DCMAKE_CXX_COMPILER=${CCDIR}/pgCC \
-DCMAKE_C_COMPILER=${CCDIR}/pgcc \
-DGMX_PREFER_STATIC_LIBS=ON \
-DGMX_MPI=OFF
make
make install
That looks fine, if you're benchmarking you might want to try the arch
specific flags - I assume PGI does have something, even if not
specific for Xeon E5.
##
I don't get any similar errors with the intel or pathscale compilers
(although intel gives me icc: command line warning #10159: invalid argument
for option '-m' a lot) and the pathscale compilation appears to be hung on
Yeah, as I sad that's kind of broken.
If anybody has run into this warning, or knows enough to be sure that I
don't need to worry about it during mdrun (it seems to be in an analysis
file, but I'm not entirely sure), then I would be happy to hear about it. A
gmx-users search for PGI returned zero results. I saw something here, but it
was not very specific about the problem with pgi (
http://www.levlafayette.com/node/175 ).
The overflow error is in the trajectory analysis tool's source files
and doesn't concern mdrun (btw, you can do make mdrun and even make
install-mdrun ;).
Would it be possible for you to share some performance numbers you're
getting on the E5?
Cheers,
--
Szilárd
Thank you,
Chris.
--
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Re: [gmx-users] compiling with the PGI compiler
On Thu, Dec 1, 2011 at 16:46, Szilárd Páll szilard.p...@cbr.su.se wrote: With the pgi compiler, I am most concerned about this floating point overflow warning: ... [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o PGC-W-0129-Floating point overflow. Check constants and constant expressions (/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/gmxlib/trajana/nbsearch.c: 166) That looks like a bug, in case of real==float HUGE_VALF should be used instead of HUGE_VAL. I'll fix that; I think the best solution is to use GMX_REAL_MAX, as HUGE_VALF isn't in C89, and might fail to compile, e.g., on Windows... I think that on most implementations, HUGE_VAL equals infinity, and thus works even in this context, but apparently not on all. And as Szilard said, this doesn't affect mdrun, only g_select at the moment. Depending a bit on what the compiler does, it might even work correctly despite the warning. Teemu -- 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] compiling with the PGI compiler
On Thu, Dec 1, 2011 at 4:49 PM, Teemu Murtola teemu.murt...@cbr.su.se wrote: On Thu, Dec 1, 2011 at 16:46, Szilárd Páll szilard.p...@cbr.su.se wrote: With the pgi compiler, I am most concerned about this floating point overflow warning: ... [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o PGC-W-0129-Floating point overflow. Check constants and constant expressions (/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/gmxlib/trajana/nbsearch.c: 166) That looks like a bug, in case of real==float HUGE_VALF should be used instead of HUGE_VAL. I'll fix that; I think the best solution is to use GMX_REAL_MAX, as HUGE_VALF isn't in C89, and might fail to compile, e.g., on Windows... I think that on most implementations, HUGE_VAL equals infinity, and thus works even in this context, but apparently not on all. And as Szilard said, this doesn't affect mdrun, only g_select at the moment. Depending a bit on what the compiler does, it might even work correctly despite the warning. Great! I was about to submit the same fix to Gerrit, good that I checked back... -- Szilárd Teemu -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] density map in 3 Dimension
Dear gromacs-users, I thought of sending this query again as I did not get any response in my last email. I was wondering whether there is any way to calculate the 3D density map of a particular selection of protein-water system ( say the water near the protein backbone) in gromacs. I guess g_densmap provides a 2D map of the density. But I was looking for 3D map of density. I presume it might have to do with calculating volume of a space. But, I am not sure how to do it in gromacs. Any help will be appreciated. Jagannath-- 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] editconf -d
Dear Prof. May I know the best quantity for -d option in editconf program? for example for a cubic box consists of 7 water molecules and 500 surfactant molecules with 22 , 022 , 22 box dimensions in x , y and z? Best Regards Sara -- 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] Fw: editconf -d
- Forwarded Message - From: mohammad agha mra...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Thursday, December 1, 2011 10:48 PM Subject: editconf -d Dear Prof. May I know the best quantity for -d option in editconf program? for example for a cubic box consists of 7 water molecules and 500 surfactant molecules with 22 , 22 , 22 box dimensions in x , y and z? Best Regards Sara-- 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] editconf -d
mohammad agha wrote: Dear Prof. May I know the best quantity for -d option in editconf program? for example for a cubic box consists of 7 water molecules and 500 surfactant molecules with 22 , 022 , 22 box dimensions in x , y and z? If you've got a box built, what's the need for -d? The purpose of setting a value with -d is to define a unit cell around a solute such that it does not interact with its periodic image during the simulation. The value is, to some extent, controlled by the cutoff values used during MD. -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] density map in 3 Dimension
jagannath mondal wrote: Dear gromacs-users, I thought of sending this query again as I did not get any response in my last email. I was wondering whether there is any way to calculate the 3D density map of a particular selection of protein-water system ( say the water near the protein backbone) in gromacs. I guess g_densmap provides a 2D map of the density. But I was looking for 3D map of density. I presume it might have to do with calculating volume of a space. But, I am not sure how to do it in gromacs. Any help will be appreciated. Two approaches come to mind: 1. Run g_densmap in all directions (invoking the -aver flag to change the dimension over which averaging is done), then somehow post-processing the output from the .xpm files into something meaningful. That will involve a lot of scripting to parse out values from the .xpm files (which are translated from the various letters of the color scheme) and then assembling some sort of meaningful format for the output. Doesn't sound to me like a trivial task, but perhaps it could be done. 2. Use g_select to define dynamic indices for water molecules that fit some geometric criterion, then feed these index groups into the individual frames of your trajectory (analyzed separately, since the index groups need not be of the same size), and again assemble some type of meaningful output from the probabilities or densities in (x,y,z) space. I've never tried either of these nor do I have anything more specific to recommend, just the general workflow of thinking out loud ;) -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] Re: Protein ligand simulation
Hi, I am trying the simulation of a docked complex of my protein . While solvating the box using the following command :- genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro The processing does not stop and continues to run . Here's the output that I got while solvating the box , which is still continuing :- Reading solute configuration GRoups of Organic Molecules in ACtion for Science Containing 3620 atoms in 231 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 46x46x46 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 21024576 residues Calculating Overlap... box_margin = 0.315 Removed 1047843 atoms that were outside the box What have gone wrong for solvation to take this much time on 12 processors CPU. -- Bharat -- 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: Protein ligand simulation
On 2/12/2011 12:37 PM, bharat gupta wrote: Hi, I am trying the simulation of a docked complex of my protein . While solvating the box using the following command :- genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro The processing does not stop and continues to run . Here's the output that I got while solvating the box , which is still continuing :- Reading solute configuration GRoups of Organic Molecules in ACtion for Science Containing 3620 atoms in 231 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 46x46x46 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 21024576 residues This is 21 million water molecules, from far too many boxes for a 3K atom protein. A few tens of thousands of water molecules would be normal. Something is wrong with the coordinates or box dimensions of your -cp file. Calculating Overlap... box_margin = 0.315 Removed 1047843 atoms that were outside the box What have gone wrong for solvation to take this much time on 12 processors CPU. All water atoms have to be tested for overlap with all protein atoms - that's expensive. Also, no GROMACS tools apart from mdrun actually use more than one processor of those available. 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: Protein ligand simulation
bharat gupta wrote: Hi, I am trying the simulation of a docked complex of my protein . While solvating the box using the following command :- genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro The processing does not stop and continues to run . Here's the output that I got while solvating the box , which is still continuing :- Reading solute configuration GRoups of Organic Molecules in ACtion for Science Containing 3620 atoms in 231 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 46x46x46 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 21024576 residues Calculating Overlap... box_margin = 0.315 Removed 1047843 atoms that were outside the box What have gone wrong for solvation to take this much time on 12 processors CPU. genbox is not parallelized; you can only use 1 CPU. You've added 21 million water molecules (yikes!) to the box and genbox is trying to remove over 1 million atoms - I'd say your box is much too large for a solute of 3620 atoms, by several orders of magnitude. You're probably running out of memory to do this operation. -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] Re: Protein ligand simulation
Actually I check the file newbox.gro in VMD and I found that the phosphate ion instead of being docked to my protein lies somewhere far away from the protein. The docked complex was taken from autodock's docking result. So what could have wrong . I guess this could be the reason for the box being too large . On Fri, Dec 2, 2011 at 10:54 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Hi, I am trying the simulation of a docked complex of my protein . While solvating the box using the following command :- genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro The processing does not stop and continues to run . Here's the output that I got while solvating the box , which is still continuing :- Reading solute configuration GRoups of Organic Molecules in ACtion for Science Containing 3620 atoms in 231 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-**MODEL,300K,BOX(M)=1.86206NM,**WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 46x46x46 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 21024576 residues Calculating Overlap... box_margin = 0.315 Removed 1047843 atoms that were outside the box What have gone wrong for solvation to take this much time on 12 processors CPU. genbox is not parallelized; you can only use 1 CPU. You've added 21 million water molecules (yikes!) to the box and genbox is trying to remove over 1 million atoms - I'd say your box is much too large for a solute of 3620 atoms, by several orders of magnitude. You're probably running out of memory to do this operation. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] Re: Protein ligand simulation
bharat gupta wrote: Actually I check the file newbox.gro in VMD and I found that the phosphate ion instead of being docked to my protein lies somewhere far away from the protein. The docked complex was taken from autodock's docking result. So what could have wrong . I guess this could be the reason for the box being too large . Sounds like you chose Autodock's undocked complex where the protein and ligand are far apart, but that's more of an Autodock question rather than a Gromacs one. -Justin On Fri, Dec 2, 2011 at 10:54 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Hi, I am trying the simulation of a docked complex of my protein . While solvating the box using the following command :- genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro The processing does not stop and continues to run . Here's the output that I got while solvating the box , which is still continuing :- Reading solute configuration GRoups of Organic Molecules in ACtion for Science Containing 3620 atoms in 231 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-__MODEL,300K,BOX(M)=1.86206NM,__WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 46x46x46 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 21024576 residues Calculating Overlap... box_margin = 0.315 Removed 1047843 atoms that were outside the box What have gone wrong for solvation to take this much time on 12 processors CPU. genbox is not parallelized; you can only use 1 CPU. You've added 21 million water molecules (yikes!) to the box and genbox is trying to remove over 1 million atoms - I'd say your box is much too large for a solute of 3620 atoms, by several orders of magnitude. You're probably running out of memory to do this operation. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://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 mailto:monu46...@yahoo.com -- 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] Re: Protein ligand simulation
I checked the docked structure and the structure obtained after adding the ligand coordinates to the processed file obtained after using pdb2gmx command. It's very surprising that in the docked structure ligand is at the correct place but the processed gromacs file the ligand lies far apart from the protein. Any clue what could be the reason for this ?? On Fri, Dec 2, 2011 at 11:00 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Actually I check the file newbox.gro in VMD and I found that the phosphate ion instead of being docked to my protein lies somewhere far away from the protein. The docked complex was taken from autodock's docking result. So what could have wrong . I guess this could be the reason for the box being too large . Sounds like you chose Autodock's undocked complex where the protein and ligand are far apart, but that's more of an Autodock question rather than a Gromacs one. -Justin On Fri, Dec 2, 2011 at 10:54 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Hi, I am trying the simulation of a docked complex of my protein . While solvating the box using the following command :- genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro The processing does not stop and continues to run . Here's the output that I got while solvating the box , which is still continuing :- Reading solute configuration GRoups of Organic Molecules in ACtion for Science Containing 3620 atoms in 231 residues Initialising van der waals distances... WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. Reading solvent configuration 216H2O,WATJP01,SPC216,SPC-__**MODEL,300K,BOX(M)=1.86206NM,__** WFVG,MAR. 1984 solvent configuration contains 648 atoms in 216 residues Initialising van der waals distances... Will generate new solvent configuration of 46x46x46 boxes Generating configuration Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 21024576 residues Calculating Overlap... box_margin = 0.315 Removed 1047843 atoms that were outside the box What have gone wrong for solvation to take this much time on 12 processors CPU. genbox is not parallelized; you can only use 1 CPU. You've added 21 million water molecules (yikes!) to the box and genbox is trying to remove over 1 million atoms - I'd say your box is much too large for a solute of 3620 atoms, by several orders of magnitude. You're probably running out of memory to do this operation. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists 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 mailto:monu46...@yahoo.com -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA
Re: [gmx-users] Re: Protein ligand simulation
bharat gupta wrote: I checked the docked structure and the structure obtained after adding the ligand coordinates to the processed file obtained after using pdb2gmx command. It's very surprising that in the docked structure ligand is at the correct place but the processed gromacs file the ligand lies far apart from the protein. Any clue what could be the reason for this ?? If the docked structure is correct, and the one you reassembled is incorrect, you made some mistake in putting it back together. It's impossible to say what went wrong based on the (lack of) information given. -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] Re: Protein ligand simulation
Here's the coordinate of the phosphate ion from the docked complex :- ATOM 2209 N GLY A 228 -4.491 73.252 3.100 1.00 31.50 -0.336 N ATOM 2210 HN GLY A 228 -4.765 72.618 3.850 1.00 0.00 0.164 HD ATOM 2211 CA GLY A 228 -4.817 74.668 3.205 1.00 34.50 0.189 C ATOM 2212 C GLY A 228 -6.283 75.040 3.026 1.00 36.60 0.253 C ATOM 2213 O GLY A 228 -6.638 76.216 3.151 1.00 36.80 -0.270 OA ATOM 2214 N ILE A 229 -7.109 74.064 2.647 1.00 38.60 -0.337 N ATOM 2215 HN ILE A 229 -6.718 73.136 2.484 1.00 0.00 0.164 HD ATOM 2216 CA ILE A 229 -8.556 74.256 2.452 1.00 41.10 0.159 C ATOM 2217 C ILE A 229 -9.275 73.368 3.447 1.00 43.10 0.251 C ATOM 2218 O ILE A 229 -8.856 72.229 3.655 1.00 43.60 -0.271 OA ATOM 2219 CB ILE A 229 -9.003 73.826 1.031 1.00 40.40 0.029 C ATOM 2220 CG1 ILE A 229 -8.528 74.844 0.013 1.00 40.50 0.002 C ATOM 2221 CG2 ILE A 229 -10.512 73.689 0.942 1.00 39.90 0.002 C ATOM CD1 ILE A 229 -8.610 74.327 -1.389 1.00 41.40 0.000 C ATOM 2223 N THR A 230 -10.312 73.894 4.098 1.00 45.60 -0.337 N ATOM 2224 HN THR A 230 -10.544 74.877 3.957 1.00 0.00 0.164 HD ATOM 2225 CA THR A 230 -11.129 73.085 5.017 1.00 47.90 0.172 C ATOM 2226 C THR A 230 -12.555 72.789 4.490 1.00 49.10 0.232 C ATOM 2227 O THR A 230 -12.945 71.602 4.523 1.00 50.90 -0.286 OA ATOM 2228 CB THR A 230 -11.179 73.714 6.460 1.00 48.20 0.139 C ATOM 2229 OG1 THR A 230 -11.348 75.136 6.384 1.00 48.60 -0.383 OA ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00 0.00 0.210 HD ATOM 2231 CG2 THR A 230 -9.880 73.414 7.220 1.00 49.10 0.034 C TER2232 THR A 230 HETATM1 P PO4 A 322 28.148 82.525 1.696 1.00 2.95 0.437 P HETATM2 O1 PO4 A 322 27.246 83.314 2.595 1.00 5.93 -0.609 OA HETATM3 O2 PO4 A 322 27.419 81.238 1.254 1.00 4.49 -0.609 OA HETATM4 O3 PO4 A 322 28.535 83.301 0.471 1.00 2.00 -0.609 OA HETATM5 O4 PO4 A 322 29.451 82.186 2.489 1.00 4.00 -0.609 OA Here's the coordinates of the processed file after adding ligand coordinates :- 230THR N 3601 -1.031 7.389 0.410 230THR HN 3602 -1.054 7.486 0.396 230THR CA 3603 -1.113 7.308 0.502 230THR HA 3604 -1.063 7.222 0.502 230THR CB 3605 -1.118 7.371 0.646 230THR HB 3606 -1.197 7.338 0.697 230THROG1 3607 -1.135 7.514 0.638 230THRHG1 3608 -1.138 7.552 0.731 230THRCG2 3609 -0.988 7.341 0.722 230THR HG21 3610 -0.993 7.382 0.813 230THR HG22 3611 -0.976 7.242 0.730 230THR HG23 3612 -0.910 7.380 0.672 230THR C 3613 -1.255 7.279 0.449 230THROT1 3614 -1.294 7.160 0.452 230THROT2 3615 -1.337 7.205 0.529 1LIG P 1 28.261 82.425 1.961 1LIG O1 2 27.805 80.999 1.894 1LIG O2 3 28.523 82.938 0.528 1LIG O3 4 27.235 83.311 2.606 1LIG O4 5 29.563 82.481 2.823 5.23907 4.16174 3.66560 On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: I checked the docked structure and the structure obtained after adding the ligand coordinates to the processed file obtained after using pdb2gmx command. It's very surprising that in the docked structure ligand is at the correct place but the processed gromacs file the ligand lies far apart from the protein. Any clue what could be the reason for this ?? If the docked structure is correct, and the one you reassembled is incorrect, you made some mistake in putting it back together. It's impossible to say what went wrong based on the (lack of) information given. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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
Re: [gmx-users] Re: Protein ligand simulation
bharat gupta wrote: Here's the coordinate of the phosphate ion from the docked complex :- ATOM 2209 N GLY A 228 -4.491 73.252 3.100 1.00 31.50 -0.336 N ATOM 2210 HN GLY A 228 -4.765 72.618 3.850 1.00 0.00 0.164 HD ATOM 2211 CA GLY A 228 -4.817 74.668 3.205 1.00 34.50 0.189 C ATOM 2212 C GLY A 228 -6.283 75.040 3.026 1.00 36.60 0.253 C ATOM 2213 O GLY A 228 -6.638 76.216 3.151 1.00 36.80 -0.270 OA ATOM 2214 N ILE A 229 -7.109 74.064 2.647 1.00 38.60 -0.337 N ATOM 2215 HN ILE A 229 -6.718 73.136 2.484 1.00 0.00 0.164 HD ATOM 2216 CA ILE A 229 -8.556 74.256 2.452 1.00 41.10 0.159 C ATOM 2217 C ILE A 229 -9.275 73.368 3.447 1.00 43.10 0.251 C ATOM 2218 O ILE A 229 -8.856 72.229 3.655 1.00 43.60 -0.271 OA ATOM 2219 CB ILE A 229 -9.003 73.826 1.031 1.00 40.40 0.029 C ATOM 2220 CG1 ILE A 229 -8.528 74.844 0.013 1.00 40.50 0.002 C ATOM 2221 CG2 ILE A 229 -10.512 73.689 0.942 1.00 39.90 0.002 C ATOM CD1 ILE A 229 -8.610 74.327 -1.389 1.00 41.40 0.000 C ATOM 2223 N THR A 230 -10.312 73.894 4.098 1.00 45.60 -0.337 N ATOM 2224 HN THR A 230 -10.544 74.877 3.957 1.00 0.00 0.164 HD ATOM 2225 CA THR A 230 -11.129 73.085 5.017 1.00 47.90 0.172 C ATOM 2226 C THR A 230 -12.555 72.789 4.490 1.00 49.10 0.232 C ATOM 2227 O THR A 230 -12.945 71.602 4.523 1.00 50.90 -0.286 OA ATOM 2228 CB THR A 230 -11.179 73.714 6.460 1.00 48.20 0.139 C ATOM 2229 OG1 THR A 230 -11.348 75.136 6.384 1.00 48.60 -0.383 OA ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00 0.00 0.210 HD ATOM 2231 CG2 THR A 230 -9.880 73.414 7.220 1.00 49.10 0.034 C TER2232 THR A 230 HETATM1 P PO4 A 322 28.148 82.525 1.696 1.00 2.95 0.437 P HETATM2 O1 PO4 A 322 27.246 83.314 2.595 1.00 5.93 -0.609 OA HETATM3 O2 PO4 A 322 27.419 81.238 1.254 1.00 4.49 -0.609 OA HETATM4 O3 PO4 A 322 28.535 83.301 0.471 1.00 2.00 -0.609 OA HETATM5 O4 PO4 A 322 29.451 82.186 2.489 1.00 4.00 -0.609 OA Here's the coordinates of the processed file after adding ligand coordinates :- 230THR N 3601 -1.031 7.389 0.410 230THR HN 3602 -1.054 7.486 0.396 230THR CA 3603 -1.113 7.308 0.502 230THR HA 3604 -1.063 7.222 0.502 230THR CB 3605 -1.118 7.371 0.646 230THR HB 3606 -1.197 7.338 0.697 230THROG1 3607 -1.135 7.514 0.638 230THRHG1 3608 -1.138 7.552 0.731 230THRCG2 3609 -0.988 7.341 0.722 230THR HG21 3610 -0.993 7.382 0.813 230THR HG22 3611 -0.976 7.242 0.730 230THR HG23 3612 -0.910 7.380 0.672 230THR C 3613 -1.255 7.279 0.449 230THROT1 3614 -1.294 7.160 0.452 230THROT2 3615 -1.337 7.205 0.529 1LIG P 1 28.261 82.425 1.961 1LIG O1 2 27.805 80.999 1.894 1LIG O2 3 28.523 82.938 0.528 1LIG O3 4 27.235 83.311 2.606 1LIG O4 5 29.563 82.481 2.823 5.23907 4.16174 3.66560 Your PO4 coordinates are still in Angstrom. They should be nm for a .gro file. -Justin On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: I checked the docked structure and the structure obtained after adding the ligand coordinates to the processed file obtained after using pdb2gmx command. It's very surprising that in the docked structure ligand is at the correct place but the processed gromacs file the ligand lies far apart from the protein. Any clue what could be the reason for this ?? If the docked structure is correct, and the one you reassembled is incorrect, you made some mistake in putting it back together. It's impossible to say what went wrong based on the (lack of) information given. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] Re: Protein ligand simulation
Sorry to ask this , but what could be done as I don't understand how could have happened?? On Fri, Dec 2, 2011 at 11:24 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Here's the coordinate of the phosphate ion from the docked complex :- ATOM 2209 N GLY A 228 -4.491 73.252 3.100 1.00 31.50 -0.336 N ATOM 2210 HN GLY A 228 -4.765 72.618 3.850 1.00 0.00 0.164 HD ATOM 2211 CA GLY A 228 -4.817 74.668 3.205 1.00 34.50 0.189 C ATOM 2212 C GLY A 228 -6.283 75.040 3.026 1.00 36.60 0.253 C ATOM 2213 O GLY A 228 -6.638 76.216 3.151 1.00 36.80-0.270 OA ATOM 2214 N ILE A 229 -7.109 74.064 2.647 1.00 38.60 -0.337 N ATOM 2215 HN ILE A 229 -6.718 73.136 2.484 1.00 0.00 0.164 HD ATOM 2216 CA ILE A 229 -8.556 74.256 2.452 1.00 41.10 0.159 C ATOM 2217 C ILE A 229 -9.275 73.368 3.447 1.00 43.10 0.251 C ATOM 2218 O ILE A 229 -8.856 72.229 3.655 1.00 43.60-0.271 OA ATOM 2219 CB ILE A 229 -9.003 73.826 1.031 1.00 40.40 0.029 C ATOM 2220 CG1 ILE A 229 -8.528 74.844 0.013 1.00 40.50 0.002 C ATOM 2221 CG2 ILE A 229 -10.512 73.689 0.942 1.00 39.90 0.002 C ATOM CD1 ILE A 229 -8.610 74.327 -1.389 1.00 41.40 0.000 C ATOM 2223 N THR A 230 -10.312 73.894 4.098 1.00 45.60-0.337 N ATOM 2224 HN THR A 230 -10.544 74.877 3.957 1.00 0.00 0.164 HD ATOM 2225 CA THR A 230 -11.129 73.085 5.017 1.00 47.90 0.172 C ATOM 2226 C THR A 230 -12.555 72.789 4.490 1.00 49.10 0.232 C ATOM 2227 O THR A 230 -12.945 71.602 4.523 1.00 50.90-0.286 OA ATOM 2228 CB THR A 230 -11.179 73.714 6.460 1.00 48.20 0.139 C ATOM 2229 OG1 THR A 230 -11.348 75.136 6.384 1.00 48.60 -0.383 OA ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00 0.00 0.210 HD ATOM 2231 CG2 THR A 230 -9.880 73.414 7.220 1.00 49.10 0.034 C TER2232 THR A 230 HETATM1 P PO4 A 322 28.148 82.525 1.696 1.00 2.95 0.437 P HETATM2 O1 PO4 A 322 27.246 83.314 2.595 1.00 5.93-0.609 OA HETATM3 O2 PO4 A 322 27.419 81.238 1.254 1.00 4.49 -0.609 OA HETATM4 O3 PO4 A 322 28.535 83.301 0.471 1.00 2.00 -0.609 OA HETATM5 O4 PO4 A 322 29.451 82.186 2.489 1.00 4.00 -0.609 OA Here's the coordinates of the processed file after adding ligand coordinates :- 230THR N 3601 -1.031 7.389 0.410 230THR HN 3602 -1.054 7.486 0.396 230THR CA 3603 -1.113 7.308 0.502 230THR HA 3604 -1.063 7.222 0.502 230THR CB 3605 -1.118 7.371 0.646 230THR HB 3606 -1.197 7.338 0.697 230THROG1 3607 -1.135 7.514 0.638 230THRHG1 3608 -1.138 7.552 0.731 230THRCG2 3609 -0.988 7.341 0.722 230THR HG21 3610 -0.993 7.382 0.813 230THR HG22 3611 -0.976 7.242 0.730 230THR HG23 3612 -0.910 7.380 0.672 230THR C 3613 -1.255 7.279 0.449 230THROT1 3614 -1.294 7.160 0.452 230THROT2 3615 -1.337 7.205 0.529 1LIG P 1 28.261 82.425 1.961 1LIG O1 2 27.805 80.999 1.894 1LIG O2 3 28.523 82.938 0.528 1LIG O3 4 27.235 83.311 2.606 1LIG O4 5 29.563 82.481 2.823 5.23907 4.16174 3.66560 Your PO4 coordinates are still in Angstrom. They should be nm for a .gro file. -Justin On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: I checked the docked structure and the structure obtained after adding the ligand coordinates to the processed file obtained after using pdb2gmx command. It's very surprising that in the docked structure ligand is at the correct place but the processed gromacs file the ligand lies far apart from the protein. Any clue what could be the reason for this ?? If the docked structure is correct, and the one you reassembled is incorrect, you made some mistake in putting it back together. It's impossible to say what went wrong based on the (lack of) information given. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing list
Re: [gmx-users] Re: Protein ligand simulation
bharat gupta wrote: Sorry to ask this , but what could be done as I don't understand how could have happened?? I'll assume that you processed your .pdb file with pdb2gmx to get the protein coordinates in .gro format, but I don't know how you added the ligand coordinates to the .gro file. If you did it by hand (i.e. copy/paste with a text editor), then you didn't preserve the required units. If you used some other program (i.e. editconf) and it did not perform as expected, that is a separate issue. Since I'm left to guess (you still haven't described exactly what you've done to construct the file), that's all I can offer. -Justin On Fri, Dec 2, 2011 at 11:24 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Here's the coordinate of the phosphate ion from the docked complex :- ATOM 2209 N GLY A 228 -4.491 73.252 3.100 1.00 31.50-0.336 N ATOM 2210 HN GLY A 228 -4.765 72.618 3.850 1.00 0.00 0.164 HD ATOM 2211 CA GLY A 228 -4.817 74.668 3.205 1.00 34.50 0.189 C ATOM 2212 C GLY A 228 -6.283 75.040 3.026 1.00 36.60 0.253 C ATOM 2213 O GLY A 228 -6.638 76.216 3.151 1.00 36.80-0.270 OA ATOM 2214 N ILE A 229 -7.109 74.064 2.647 1.00 38.60-0.337 N ATOM 2215 HN ILE A 229 -6.718 73.136 2.484 1.00 0.00 0.164 HD ATOM 2216 CA ILE A 229 -8.556 74.256 2.452 1.00 41.10 0.159 C ATOM 2217 C ILE A 229 -9.275 73.368 3.447 1.00 43.10 0.251 C ATOM 2218 O ILE A 229 -8.856 72.229 3.655 1.00 43.60-0.271 OA ATOM 2219 CB ILE A 229 -9.003 73.826 1.031 1.00 40.40 0.029 C ATOM 2220 CG1 ILE A 229 -8.528 74.844 0.013 1.00 40.50 0.002 C ATOM 2221 CG2 ILE A 229 -10.512 73.689 0.942 1.00 39.90 0.002 C ATOM CD1 ILE A 229 -8.610 74.327 -1.389 1.00 41.40 0.000 C ATOM 2223 N THR A 230 -10.312 73.894 4.098 1.00 45.60-0.337 N ATOM 2224 HN THR A 230 -10.544 74.877 3.957 1.00 0.00 0.164 HD ATOM 2225 CA THR A 230 -11.129 73.085 5.017 1.00 47.90 0.172 C ATOM 2226 C THR A 230 -12.555 72.789 4.490 1.00 49.10 0.232 C ATOM 2227 O THR A 230 -12.945 71.602 4.523 1.00 50.90-0.286 OA ATOM 2228 CB THR A 230 -11.179 73.714 6.460 1.00 48.20 0.139 C ATOM 2229 OG1 THR A 230 -11.348 75.136 6.384 1.00 48.60-0.383 OA ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00 0.00 0.210 HD ATOM 2231 CG2 THR A 230 -9.880 73.414 7.220 1.00 49.10 0.034 C TER2232 THR A 230 HETATM1 P PO4 A 322 28.148 82.525 1.696 1.00 2.95 0.437 P HETATM2 O1 PO4 A 322 27.246 83.314 2.595 1.00 5.93-0.609 OA HETATM3 O2 PO4 A 322 27.419 81.238 1.254 1.00 4.49-0.609 OA HETATM4 O3 PO4 A 322 28.535 83.301 0.471 1.00 2.00-0.609 OA HETATM5 O4 PO4 A 322 29.451 82.186 2.489 1.00 4.00-0.609 OA Here's the coordinates of the processed file after adding ligand coordinates :- 230THR N 3601 -1.031 7.389 0.410 230THR HN 3602 -1.054 7.486 0.396 230THR CA 3603 -1.113 7.308 0.502 230THR HA 3604 -1.063 7.222 0.502 230THR CB 3605 -1.118 7.371 0.646 230THR HB 3606 -1.197 7.338 0.697 230THROG1 3607 -1.135 7.514 0.638 230THRHG1 3608 -1.138 7.552 0.731 230THRCG2 3609 -0.988 7.341 0.722 230THR HG21 3610 -0.993 7.382 0.813 230THR HG22 3611 -0.976 7.242 0.730 230THR HG23 3612 -0.910 7.380 0.672 230THR C 3613 -1.255 7.279 0.449 230THROT1 3614 -1.294 7.160 0.452 230THROT2 3615 -1.337 7.205 0.529 1LIG P 1 28.261 82.425 1.961 1LIG O1 2 27.805 80.999 1.894 1LIG O2 3 28.523 82.938 0.528 1LIG O3 4 27.235 83.311 2.606 1LIG O4 5 29.563 82.481 2.823 5.23907 4.16174 3.66560 Your PO4 coordinates are still in Angstrom. They should be nm for a .gro file. -Justin On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: I checked the docked structure
Re: [gmx-users] Re: Protein ligand simulation
Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. On Fri, Dec 2, 2011 at 11:44 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Sorry to ask this , but what could be done as I don't understand how could have happened?? I'll assume that you processed your .pdb file with pdb2gmx to get the protein coordinates in .gro format, but I don't know how you added the ligand coordinates to the .gro file. If you did it by hand (i.e. copy/paste with a text editor), then you didn't preserve the required units. If you used some other program (i.e. editconf) and it did not perform as expected, that is a separate issue. Since I'm left to guess (you still haven't described exactly what you've done to construct the file), that's all I can offer. -Justin On Fri, Dec 2, 2011 at 11:24 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Here's the coordinate of the phosphate ion from the docked complex :- ATOM 2209 N GLY A 228 -4.491 73.252 3.100 1.00 31.50-0.336 N ATOM 2210 HN GLY A 228 -4.765 72.618 3.850 1.00 0.00 0.164 HD ATOM 2211 CA GLY A 228 -4.817 74.668 3.205 1.00 34.50 0.189 C ATOM 2212 C GLY A 228 -6.283 75.040 3.026 1.00 36.60 0.253 C ATOM 2213 O GLY A 228 -6.638 76.216 3.151 1.00 36.80-0.270 OA ATOM 2214 N ILE A 229 -7.109 74.064 2.647 1.00 38.60-0.337 N ATOM 2215 HN ILE A 229 -6.718 73.136 2.484 1.00 0.00 0.164 HD ATOM 2216 CA ILE A 229 -8.556 74.256 2.452 1.00 41.10 0.159 C ATOM 2217 C ILE A 229 -9.275 73.368 3.447 1.00 43.10 0.251 C ATOM 2218 O ILE A 229 -8.856 72.229 3.655 1.00 43.60-0.271 OA ATOM 2219 CB ILE A 229 -9.003 73.826 1.031 1.00 40.40 0.029 C ATOM 2220 CG1 ILE A 229 -8.528 74.844 0.013 1.00 40.50 0.002 C ATOM 2221 CG2 ILE A 229 -10.512 73.689 0.942 1.00 39.90 0.002 C ATOM CD1 ILE A 229 -8.610 74.327 -1.389 1.00 41.40 0.000 C ATOM 2223 N THR A 230 -10.312 73.894 4.098 1.00 45.60-0.337 N ATOM 2224 HN THR A 230 -10.544 74.877 3.957 1.00 0.00 0.164 HD ATOM 2225 CA THR A 230 -11.129 73.085 5.017 1.00 47.90 0.172 C ATOM 2226 C THR A 230 -12.555 72.789 4.490 1.00 49.10 0.232 C ATOM 2227 O THR A 230 -12.945 71.602 4.523 1.00 50.90-0.286 OA ATOM 2228 CB THR A 230 -11.179 73.714 6.460 1.00 48.20 0.139 C ATOM 2229 OG1 THR A 230 -11.348 75.136 6.384 1.00 48.60-0.383 OA ATOM 2230 HG1 THR A 230 -12.152 75.322 5.914 1.00 0.00 0.210 HD ATOM 2231 CG2 THR A 230 -9.880 73.414 7.220 1.00 49.10 0.034 C TER2232 THR A 230 HETATM1 P PO4 A 322 28.148 82.525 1.696 1.00 2.95 0.437 P HETATM2 O1 PO4 A 322 27.246 83.314 2.595 1.00 5.93-0.609 OA HETATM3 O2 PO4 A 322 27.419 81.238 1.254 1.00 4.49-0.609 OA HETATM4 O3 PO4 A 322 28.535 83.301 0.471 1.00 2.00-0.609 OA HETATM5 O4 PO4 A 322 29.451 82.186 2.489 1.00 4.00-0.609 OA Here's the coordinates of the processed file after adding ligand coordinates :- 230THR N 3601 -1.031 7.389 0.410 230THR HN 3602 -1.054 7.486 0.396 230THR CA 3603 -1.113 7.308 0.502 230THR HA 3604 -1.063 7.222 0.502 230THR CB 3605 -1.118 7.371 0.646 230THR HB 3606 -1.197 7.338 0.697 230THROG1 3607 -1.135 7.514 0.638 230THRHG1 3608 -1.138 7.552 0.731 230THRCG2 3609 -0.988 7.341 0.722 230THR HG21 3610 -0.993 7.382 0.813 230THR HG22 3611 -0.976 7.242 0.730 230THR HG23 3612 -0.910 7.380 0.672 230THR C 3613 -1.255 7.279 0.449 230THROT1 3614 -1.294 7.160 0.452 230THROT2 3615 -1.337 7.205 0.529 1LIG P 1 28.261 82.425 1.961 1LIG O1 2 27.805 80.999 1.894 1LIG O2 3 28.523 82.938 0.528 1LIG O3 4 27.235 83.311 2.606 1LIG O4 5 29.563 82.481 2.823 5.23907 4.16174 3.66560 Your PO4 coordinates are still in Angstrom. They should be nm for a .gro file. -Justin On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Re: [gmx-users] Re: Protein ligand simulation
bharat gupta wrote: Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. Then you prepared it incorrectly. You need to use the right units. -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] Re: Protein ligand simulation
Sorry I didn't understand . Can u brief it ?? On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. Then you prepared it incorrectly. You need to use the right units. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] Re: Protein ligand simulation
bharat gupta wrote: Sorry I didn't understand . Can u brief it ?? I already did: http://lists.gromacs.org/pipermail/gmx-users/2011-December/04.html -Justin On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. Then you prepared it incorrectly. You need to use the right units. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://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 mailto:monu46...@yahoo.com -- 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] Failed to lock .log. Already running simulation?
Dear Users: I have 50 simulations that are all the same, except with different random seeds for velocities. All were running fine for 24 hours. I canceled the running jobs and resubmitted them as part of beta testing a new cluster. All 50 started. I then canceled one of these jobs soon after starting it and then started it again pretty quickly (possibly too quickly). This restart now gave me the error: Fatal error: Failed to lock: continue.log. Already running simulation? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I found this post about this possibly being related to the Lustre filesystem: http://lists.gromacs.org/pipermail/gmx-users/2010-November/056173.html But I am not sure how to figure out if that is being used. Here is the output from mount: [nealechr@ip13-mp2 50]$ mount /dev/mapper/hddvg-root on / type ext4 (rw) proc on /proc type proc (rw) sysfs on /sys type sysfs (rw) devpts on /dev/pts type devpts (rw,gid=5,mode=620) tmpfs on /dev/shm type tmpfs (rw) /dev/md0 on /boot type ext4 (rw) /dev/mapper/hddvg-home on /home type ext4 (rw,usrquota,grpquota) /dev/md2 on /ltmp type ext4 (rw) /dev/mapper/hddvg-opt on /opt type ext4 (rw) none on /ramdisk type tmpfs (rw,nosuid,nodev) none on /var/tmp type tmpfs (rw,noexec,nosuid,nodev,size=10) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) none on /ipathfs type ipathfs (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) nfsd on /proc/fs/nfsd type nfsd (rw) none on /tmp type tmpfs (rw,noexec,nosuid,nodev,size=10) 10.4.215.201@o2ib:/lustre01 on /mnt/scratch01 type lustre (rw,_netdev,flock) Also, it seems unlikely to be system related because the other 49 runs are going just fine. I did a ls -la to see if there was some hidden file to indicate the lock but could not find any (I have no idea how such a lock would work or be detected). I deleted the .log file, but then I get the error: Fatal error: File appending requested, but only 3 of the 4 output files are present Moving everything to a new directory and then copying it back (including the original .log file) allowed me to run the simulation. Did I do something incorrectly, or is this a bona-fide problem? Thank you, Chris. -- 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: Protein ligand simulation
I didn't understand what you meant by that link. Can you please tell me what can be done ?? On Fri, Dec 2, 2011 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Sorry I didn't understand . Can u brief it ?? I already did: http://lists.gromacs.org/**pipermail/gmx-users/2011-**December/04.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2011-December/04.html -Justin On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. Then you prepared it incorrectly. You need to use the right units. -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists 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 mailto:monu46...@yahoo.com -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] Re: Protein ligand simulation
One file you used had the coordinates in angstroms, the other in nanometers. You cannot have numbers with different units in the same coordinate file. Which is what you did. Hence why they are not in the locations you assumed they were. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of bharat gupta Sent: Friday, 2 December 2011 3:22 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Re: Protein ligand simulation I didn't understand what you meant by that link. Can you please tell me what can be done ?? On Fri, Dec 2, 2011 at 11:52 AM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu wrote: bharat gupta wrote: Sorry I didn't understand . Can u brief it ?? I already did: http://lists.gromacs.org/pipermail/gmx-users/2011-December/04.html -Justin On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu mailto:jalem...@vt.edumailto:jalem...@vt.edu wrote: bharat gupta wrote: Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. Then you prepared it incorrectly. You need to use the right units. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-users@gromacs.orgmailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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.orgmailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://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.commailto:monu46...@yahoo.com mailto:monu46...@yahoo.commailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-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.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://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.commailto: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] Re: Protein ligand simulation
Yes, but I took the coordinates for phosphate ion from some other pdb file and docked with my protein using autodock. Then I generated the parameter for the ion using swissparam. Then prepared the protein file using pdb2gmx and pasted the coordinates of docked ion from the docked file obtained from autodock. What Shall I do now ?? ... On Fri, Dec 2, 2011 at 1:35 PM, Dallas Warren dallas.war...@monash.eduwrote: One file you used had the coordinates in angstroms, the other in nanometers. ** ** You cannot have numbers with different units in the same coordinate file. Which is what you did. Hence why they are not in the locations you assumed they were. ** ** Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. ** ** *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *bharat gupta *Sent:* Friday, 2 December 2011 3:22 PM *To:* jalem...@vt.edu; Discussion list for GROMACS users *Subject:* Re: [gmx-users] Re: Protein ligand simulation ** ** I didn't understand what you meant by that link. Can you please tell me what can be done ?? On Fri, Dec 2, 2011 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu wrote: bharat gupta wrote: Sorry I didn't understand . Can u brief it ?? ** ** I already did: http://lists.gromacs.org/pipermail/gmx-users/2011-December/04.html -Justin On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: bharat gupta wrote: Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. Then you prepared it incorrectly. You need to use the right units. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://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 mailto:monu46...@yahoo.com -- 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 -- 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] Re: Protein ligand simulation
On 2/12/2011 3:41 PM, bharat gupta wrote: Yes, but I took the coordinates for phosphate ion from some other pdb file and docked with my protein using autodock. Then I generated the parameter for the ion using swissparam. Then prepared the protein file using pdb2gmx and pasted the coordinates of docked ion from the docked file obtained from autodock. What Shall I do now ?? ... Don't paste apples with oranges and feed them to a program in a format that specifies only apples. Convert the units. Mark On Fri, Dec 2, 2011 at 1:35 PM, Dallas Warren dallas.war...@monash.edu mailto:dallas.war...@monash.edu wrote: One file you used had the coordinates in angstroms, the other in nanometers. You cannot have numbers with different units in the same coordinate file. Which is what you did. Hence why they are not in the locations you assumed they were. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu mailto:dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:*gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *bharat gupta *Sent:* Friday, 2 December 2011 3:22 PM *To:* jalem...@vt.edu mailto:jalem...@vt.edu; Discussion list for GROMACS users *Subject:* Re: [gmx-users] Re: Protein ligand simulation I didn't understand what you meant by that link. Can you please tell me what can be done ?? On Fri, Dec 2, 2011 at 11:52 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Sorry I didn't understand . Can u brief it ?? I already did: http://lists.gromacs.org/pipermail/gmx-users/2011-December/04.html -Justin On Fri, Dec 2, 2011 at 11:47 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: bharat gupta wrote: Yes, I prepared the protein file separately using pdb2gmx and then I pasted the ligand manually from the docked file. Then you prepared it incorrectly. You need to use the right units. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://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 mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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
[gmx-users] (no subject)
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