[gmx-users] How to calculate enthalpy
Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ? Can we calculate enthapy from g_energy? -- 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 to calculate enthalpy
Thanks Vitaly but how?? let's say the difference between unfolded to folded protein is 100 water molecules. What is the correct procedure to calculate (theoretically) the entrapy correspond to single water molecule for stabilizing/destabilizing the protein. help me > Sure, you can. > > > > Dr. Vitaly V. Chaban > > > On Mon, Jul 15, 2013 at 8:38 AM, wrote: > >> Hi >> >> I want calculate the enthalpy of water molecule corresponding to protein >> folded and unfolded state. >> How much a single water molecule (enthalpy and free energy) contribute >> in >> folding ? >> Can we calculate enthapy from g_energy? >> >> >> >> -- >> 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 > -- 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] entropy calculation
Hi gmx users I took a natural protein fold and unfolded with simulated annealing molecular dynamics (SAMD). Now I have folded and unfolded structure. I want to calculate statistically entropy difference of the two system. Can we do with gromacs??? what is the correct protocol ?? best pooja -- 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] entropy calculation
Thanks Justin > > > On 7/16/13 4:30 AM, pooja_gu...@nccs.res.in wrote: >> Hi gmx users >> >> I took a natural protein fold and unfolded with simulated annealing >> molecular dynamics (SAMD). Now I have folded and unfolded structure. I >> want to calculate statistically entropy difference of the two system. >> >> Can we do with gromacs??? >> what is the correct protocol ?? >> > > g_anaeig allows for the calculation of entropy based on the quasiharmonic > approach. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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 > -- Pooja Gupta, Ph.D. DBT-RA, Lab of Structural Biology National Centre for Cell Science NCCS Complex,University of Pune Campus Ganeshkhind, Pune 411007 India Email: pooja_gu...@nccs.res.in/ poojagupta@gmail.com Phone: +91-20-25708158 -- 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] entropy calculation
Hi Justin When i used g_anaeig option for the calulation, i choose system as an option i got an error "Segmentation fault (core dumped)" > > > On 7/16/13 4:30 AM, pooja_gu...@nccs.res.in wrote: >> Hi gmx users >> >> I took a natural protein fold and unfolded with simulated annealing >> molecular dynamics (SAMD). Now I have folded and unfolded structure. I >> want to calculate statistically entropy difference of the two system. >> >> Can we do with gromacs??? >> what is the correct protocol ?? >> > > g_anaeig allows for the calculation of entropy based on the quasiharmonic > approach. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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 > -- Pooja Gupta, Ph.D. DBT-RA, Lab of Structural Biology National Centre for Cell Science NCCS Complex,University of Pune Campus Ganeshkhind, Pune 411007 India Email: pooja_gu...@nccs.res.in/ poojagupta@gmail.com Phone: +91-20-25708158 -- 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] entropy calculation
thanks for reply i am using Gromacs 4.5.5 version command g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp -Pooja > > > On 7/17/13 7:28 AM, pooja_gu...@nccs.res.in wrote: >> Hi Justin >> >> When i used g_anaeig option for the calulation, i choose system as an >> option i got an error "Segmentation fault (core dumped)" > > Please provide the exact sequence of commands you used, copied and pasted > from > your terminal. Please also specify which Gromacs version you are using. > > -Justin > >>> >>> >>> On 7/16/13 4:30 AM, pooja_gu...@nccs.res.in wrote: Hi gmx users I took a natural protein fold and unfolded with simulated annealing molecular dynamics (SAMD). Now I have folded and unfolded structure. I want to calculate statistically entropy difference of the two system. Can we do with gromacs??? what is the correct protocol ?? >>> >>> g_anaeig allows for the calculation of entropy based on the >>> quasiharmonic >>> approach. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> -- >>> 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 >>> >> >> > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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] entropy calculation
I used system (0) for g-covar. Pooja > > > On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote: >> thanks for reply >> >> i am using Gromacs 4.5.5 version >> command >> g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp >> > > What was the g_covar command used to generate the eigenvector .trr file? > What > group did you choose for analysis during g_covar? > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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] extraction of PDB from clusters.pdb
try trjconv to extract the structures pooja > You can do it by using simple shell scripting > On Jul 17, 2013 12:58 AM, "Shine A" wrote: > >> Sir, >> >> Using g_cluster I clustered snapshots in md trajectory using the >> command as follows >> >> g_cluster -s sd_7.tpr -f traj7.trr -dist rmsd-distribution.xvg -o >> clusters.xpm -sz cluster-sizes.xvg -tr cluster-transitions.xpm -ntr >> cluster-transitions.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb >> -cutoff 0.25 -method gromos -dt 10 >> >> Here I got clusters.pdb having central structures in each cluster. Is >> there >> any command line option available to extract all individual files from >> clusters.pdb. >> -- >> 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 > -- 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] entropy calculation
okk This may be very basic question. I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I picked up one unfolded structure from the trj and solvated with water. I ran em for full system. now i am calculating the entropy. I afraid if i missed something. I am doing this first time. Pooja > > > On 7/17/13 7:56 AM, pooja_gu...@nccs.res.in wrote: >> I used system (0) for g-covar. >> > > Most likely, g_anaeig is running out of memory. Try using some subset of > the > system, like the protein only or its backbone. > > -Justin > >>> On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote: thanks for reply i am using Gromacs 4.5.5 version command g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp >>> >>> What was the g_covar command used to generate the eigenvector .trr >>> file? >>> What >>> group did you choose for analysis during g_covar? >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> -- >>> 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 >>> >> >> >> > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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] entropy calculation
i took only single structure > > > On 7/17/13 8:09 AM, pooja_gu...@nccs.res.in wrote: >> okk >> >> This may be very basic question. >> I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I >> picked up one unfolded structure from the trj and solvated with water. I >> ran em for full system. now i am calculating the entropy. I afraid if i >> missed something. >> > > Are you running g_covar on the original 10 ns trajectory, or on a single > energy-minimized structure? That latter would not make sense. > >> I am doing this first time. > > There is a large body of literature on configurational entropy related to > the > quasiharmonic approximation. I would suggest you look into its underlying > theory and how others apply it to biomolecular simulations. > > -Justin > >>> >>> On 7/17/13 7:56 AM, pooja_gu...@nccs.res.in wrote: I used system (0) for g-covar. >>> >>> Most likely, g_anaeig is running out of memory. Try using some subset >>> of >>> the >>> system, like the protein only or its backbone. >>> >>> -Justin >>> > On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote: >> thanks for reply >> >> i am using Gromacs 4.5.5 version >> command >> g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp >> > > What was the g_covar command used to generate the eigenvector .trr > file? > What > group did you choose for analysis during g_covar? > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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 > >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> -- >>> 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 >>> >> >> > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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 > -- Pooja Gupta, Ph.D. DBT-RA, Lab of Structural Biology National Centre for Cell Science NCCS Complex,University of Pune Campus Ganeshkhind, Pune 411007 India Email: pooja_gu...@nccs.res.in/ poojagupta@gmail.com Phone: +91-20-25708158 -- 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] entropy calculation
thank justin > > > On 7/17/13 8:19 AM, pooja_gu...@nccs.res.in wrote: >> i took only single structure >>> > > You can't calculate entropy from a single structure. Please investigate > the > literature. > > -Justin > >>> >>> On 7/17/13 8:09 AM, pooja_gu...@nccs.res.in wrote: okk This may be very basic question. I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I picked up one unfolded structure from the trj and solvated with water. I ran em for full system. now i am calculating the entropy. I afraid if i missed something. >>> >>> Are you running g_covar on the original 10 ns trajectory, or on a >>> single >>> energy-minimized structure? That latter would not make sense. >>> I am doing this first time. >>> >>> There is a large body of literature on configurational entropy related >>> to >>> the >>> quasiharmonic approximation. I would suggest you look into its >>> underlying >>> theory and how others apply it to biomolecular simulations. >>> >>> -Justin >>> > > On 7/17/13 7:56 AM, pooja_gu...@nccs.res.in wrote: >> I used system (0) for g-covar. >> > > Most likely, g_anaeig is running out of memory. Try using some > subset > of > the > system, like the protein only or its backbone. > > -Justin > >>> On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote: thanks for reply i am using Gromacs 4.5.5 version command g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp >>> >>> What was the g_covar command used to generate the eigenvector .trr >>> file? >>> What >>> group did you choose for analysis during g_covar? >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> -- >>> 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 >>> >> >> >> > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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 > >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> -- >>> 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 >>> >> >> > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > gmx-users mailing listgmx-users@gromacs.org > http
[gmx-users] script to add water in protein
Hi I want to add water molecule in my structure. Do anyone have idea how to add water molecules in protein structure. I little aware of python. How the gromacs spc216 add the water molecule. Can i get the code for the same? pooja -- 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] script to add water in protein
Thanks I am looking for code (python, C++), not gromacs command line. pooja > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html > > > On Mon, Aug 12, 2013 at 4:09 PM, wrote: > >> Hi >> >> I want to add water molecule in my structure. Do anyone have idea how to >> add water molecules in protein structure. I little aware of python. >> How the gromacs spc216 add the water molecule. Can i get the code for >> the >> same? >> >> pooja >> >> -- >> 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 > -- 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
