[gmx-users] Cytochrom C
Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? Thanks, Dariush -- 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] Cytochrom C
Yes, I have PDB file (1HRC.pdb). However, when I try to use "pdb2gmx" I get this error: Residue 'HEM' not found in residue topology database and HEM is Iron ion inside this protein. I do not know which forcefield is proper to use. I also tried MARTINI force field according their website; I used martinize.py script; Again I got error. Regards, Dariush On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> >> Hi all, >> >> Has anybody made initial configuration for Cytochrom C? Can it be shared >> with me? >> >> > There are several in the PDB. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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] RDF(PMF) and Umbrella sampling
Hi Gavin, A question arose for me: why did you consider the (rate = 0)? Dariush On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh wrote: > Hi Justin > > Just a quick clarification regarding my previous point. With geometry = > distance, and pull_dim =Y Y Y . Is the pull_group sampling all > dimensions equally (or without prejudice) about pull_init ? And iN your > first reply what did you mean about by "straight pull" ? > > Cheers > > Gavin > > Justin A. Lemkul wrote: > > > > > > Gavin Melaugh wrote: > >> Hi Justin > >> > >> Thanks for the reply. I wanted my "pulling" to be free in all > >> directions, that is in the liquid state with no defined reaction > >> coordinate i.e not along a specific axis. This is why I used geometry = > >> distance. Would you agree with this approach? > > > > I suppose there is an argument that can be made for a more free > > approach such as this one, but you're going to get the artifact you > > observed the instant your pull group moves past a zero COM distance. > > Whether or not this is a significant problem is something you'll have > > to determine. > > > > -Justin > > > >> By free I mean. The absolute distance between the COG of the ref group > >> and that of the pull group. > >> > >> Cheers > >> > >> Gavin > >> > >> Justin A. Lemkul wrote: > >>> > >>> Gavin Melaugh wrote: > >>>> Dear all > >>>> > >>>> I have a query regarding umbrella sampling simulations that I have > >>>> carried out to study a dynamical process of a guest inserting into a > >>>> host. I always get get a wall tending off to infinity at or just > >>>> before > >>>> the zero distance between the > >>>> two species. > >>>> The process I describe, for one system in particular, happens readily > >>>> and I have compared the PMF from a non constrained simulation (via the > >>>> RDF and reversible work theorem) and the same PMF from a set of > >>>> umbrella sampling > >>>> simulations. They agree quite well but in the non constrained > >>>> simulation > >>>> I get a minimum practically at zero whereas for the umbrella sampling > >>>> the minimum is shifted and there is an infinite wall close to zero. > >>>> This > >>>> wall is not present from the reversible work theorem. Why the infinite > >>>> wall? Why does the black histogram not centre around zero. Is this an > >>>> artefact of the umbrella technique? Please see attached the profile > >>>> from > >>>> the umbrella sampling technique, and the corresponding histograms. > >>>> > >>> What's happening is the COM reference distance is changing signs, so > >>> you get an artifact. The "distance" geometry is relatively inflexible > >>> and is only suitable for straight pulls of continuously increasing or > >>> continuously decreasing COM distance. You should try using the > >>> "position" geometry instead. There are some notes that you may find > >>> useful in my tutorial: > >>> > >>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html > >>> > >>> > >>> > >>> -Justin > >>> > >>>> Here is an excerpt from one of the umbrella mdp files. > >>>> > >>>> pull= umbrella > >>>> pull_geometry = distance > >>>> pull_dim = Y Y Y > >>>> pull_start = no > >>>> pull_ngroups = 1 > >>>> pull_group0 = cage_1 > >>>> pull_group1 = tail > >>>> pull_init1 = 0 > >>>> pull_rate1 = 0.0 > >>>> pull_k1 = 1 > >>>> pull_nstxout = 150 > >>>> pull_nstfout = 150 > >>>> > >>>> > >>>> Cheers > >>>> > >>>> Gavin > >>>> > >>>> > >>>> > > >>>> > >>>> > >>>> > >>>> > > >>>> > >>>> > >> > >> > > > > -- > 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 > -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Cytochrom C
I tried charmm27 too. Error: Residue 'ACE' not found in residue topology database I tried all forcefield in the list provided by "pdb2gmx", but non of them works. Dariush On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers wrote: >HEME is in the charmm27 force field. > bob h. > > > > > On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: > > Yes, I have PDB file (1HRC.pdb). However, when I try to use "pdb2gmx" I > get this error: > > Residue 'HEM' not found in residue topology database > > and HEM is Iron ion inside this protein. I do not know which forcefield is > proper to use. I also tried MARTINI force field according their website; I > used martinize.py script; Again I got error. > > Regards, > Dariush > > > > > On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul wrote: > >> >> >> Dariush Mohammadyani wrote: >> >>> >>> Hi all, >>> >>> Has anybody made initial configuration for Cytochrom C? Can it be shared >>> with me? >>> >>> >> There are several in the PDB. >> >> -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 >> > > > > > > > > -- > Robert J. Hamers > Wisconsin Distinguished Professor > Univ. of Wisconsin-Madison > 1101 University Avenue > Madison, WI 53706 > Ph: 608-262-6371 > Web: http://hamers.chem.wisc.edu > > -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Cytochrom C
Dear Peter and Krzyszto, Thank you. I am following your comments. If I get any problem I will come back. On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai wrote: > He must be using an older version of Gromacs. 4.5.4 and lower don't have > ACE in charmm27. > > On 2012-01-06 12:59:56PM -0600, Krzysztof Kuczera wrote: > > Here is the blocking group from > > gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp > > KK > > > > [ ACE ] > > [ atoms ] > > CH3 CT3 -0.270 0 > > HH31HA 0.090 1 > > HH32HA 0.090 2 > > HH33HA 0.090 3 > > C C 0.510 4 > > O O -0.510 5 > > [ bonds ] > > C CH3 > > C +N > > CH3 HH31 > > CH3 HH32 > > CH3 HH33 > > O C > > [ impropers ] > > C CH3 +N O > > > > > > On 1/6/12 12:40 PM, Peter C. Lai wrote: > > > Corrected bonds section (sorry been up all night) > > > > > > [ ACE ] > > >[ atoms ] > > > CH3CT3-0.270 > > > HH31 HA 0.091 > > > HH32 HA 0.092 > > > HH33 HA 0.093 > > > CC 0.514 > > > OO -0.515 > > >[ bonds ] > > > CH3HH31 > > > CH3HH32 > > > CH3HH33 > > > CH3C > > > C O > > > > > > Surprisingly, an .hdb entry for ACE exists so you don't need to > create one. > > > (and the .hdb entry uses HH3 as the base hydrogen name in ACE) > > > > > >> > > >> On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote: > > >>> Gromos96 53A6 has it. > > >>> > > >>> On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote: > > >>>> I tried charmm27 too. > > >>>> > > >>>> Error: > > >>>> Residue 'ACE' not found in residue topology database > > >>>> > > >>>> I tried all forcefield in the list provided by "pdb2gmx", but non > of them > > >>>> works. > > >>>> > > >>>> Dariush > > >>>> > > >>>> > > >>>> On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers > wrote: > > >>>> > > >>>>> HEME is in the charmm27 force field. > > >>>>> bob h. > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>> On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: > > >>>>> > > >>>>> Yes, I have PDB file (1HRC.pdb). However, when I try to use > "pdb2gmx" I > > >>>>> get this error: > > >>>>> > > >>>>> Residue 'HEM' not found in residue topology database > > >>>>> > > >>>>> and HEM is Iron ion inside this protein. I do not know which > forcefield is > > >>>>> proper to use. I also tried MARTINI force field according their > website; I > > >>>>> used martinize.py script; Again I got error. > > >>>>> > > >>>>> Regards, > > >>>>> Dariush > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>> On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul > wrote: > > >>>>> > > >>>>>> > > >>>>>> Dariush Mohammadyani wrote: > > >>>>>> > > >>>>>>> Hi all, > > >>>>>>> > > >>>>>>> Has anybody made initial configuration for Cytochrom C? Can it > be shared > > >>>>>>> with me? > > >>>>>>> > > >>>>>>> > > >>>>>> There are several in the PDB. > > >>>>>> > > >>>>>> -Justin > > >>>>>> > > >>>>>> -- > > >>>>>> > > >>>>>> > > >>>>>> Justin A. Lemkul > > >>>>>> Ph.D. Candidate &
Re: [gmx-users] umbrella sampling tutorial quastion
As I know, it is not necessary to restrain neither reference nor pulled group. When you apply pulling force, it means you have restrained both of them. Dariush On Mon, Jan 9, 2012 at 4:15 PM, przemek bartha wrote: > Hello, > According to Justin's tutorial on umbrella sampling, > link: > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html > could anyone explain, if the molecules are restrained in any way in the > umbrella sampling part? > What I mean, is when we pull molecule A from molecule B, we restrain "B" > to that it does not follow "A" (by adding "pos_res" section in .itp file). > In my particular case, I pull asparagin asid (ASP) from lisyne (LYS), so I > have got two .itp files for both molecules. Restraining LYS worked well for > generating configurations, but failed for umbrella sampling. > My molecules (including LYS which was restrained) were "flying" randomly > all over the box which resulted in incorrect PMF courve. > > So, during umbrella sampling, shall both the molecules be restrained, > none, or only one of them? Why? > > thanks in advance, > Przemek > > -- > 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 > -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Cytochrom C
Does anybody know where can I find [ HIS ] parameters? Thanks, Dariush On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani < d.mohammady...@gmail.com> wrote: > Dear Peter and Krzyszto, > > Thank you. I am following your comments. If I get any problem I will come > back. > > > > > On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai wrote: > >> He must be using an older version of Gromacs. 4.5.4 and lower don't have >> ACE in charmm27. >> >> On 2012-01-06 12:59:56PM -0600, Krzysztof Kuczera wrote: >> > Here is the blocking group from >> > gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp >> > KK >> > >> > [ ACE ] >> > [ atoms ] >> > CH3 CT3 -0.270 0 >> > HH31HA 0.090 1 >> > HH32HA 0.090 2 >> > HH33HA 0.090 3 >> > C C 0.510 4 >> > O O -0.510 5 >> > [ bonds ] >> > C CH3 >> > C +N >> > CH3 HH31 >> > CH3 HH32 >> > CH3 HH33 >> > O C >> > [ impropers ] >> > C CH3 +N O >> > >> > >> > On 1/6/12 12:40 PM, Peter C. Lai wrote: >> > > Corrected bonds section (sorry been up all night) >> > > >> > > [ ACE ] >> > >[ atoms ] >> > > CH3CT3-0.270 >> > > HH31 HA 0.091 >> > > HH32 HA 0.092 >> > > HH33 HA 0.093 >> > > CC 0.514 >> > > OO -0.515 >> > >[ bonds ] >> > > CH3 HH31 >> > > CH3HH32 >> > > CH3HH33 >> > > CH3C >> > > C O >> > > >> > > Surprisingly, an .hdb entry for ACE exists so you don't need to >> create one. >> > > (and the .hdb entry uses HH3 as the base hydrogen name in ACE) >> > > >> > >> >> > >> On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote: >> > >>> Gromos96 53A6 has it. >> > >>> >> > >>> On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote: >> > >>>> I tried charmm27 too. >> > >>>> >> > >>>> Error: >> > >>>> Residue 'ACE' not found in residue topology database >> > >>>> >> > >>>> I tried all forcefield in the list provided by "pdb2gmx", but non >> of them >> > >>>> works. >> > >>>> >> > >>>> Dariush >> > >>>> >> > >>>> >> > >>>> On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers >> wrote: >> > >>>> >> > >>>>> HEME is in the charmm27 force field. >> > >>>>> bob h. >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: >> > >>>>> >> > >>>>> Yes, I have PDB file (1HRC.pdb). However, when I try to use >> "pdb2gmx" I >> > >>>>> get this error: >> > >>>>> >> > >>>>> Residue 'HEM' not found in residue topology database >> > >>>>> >> > >>>>> and HEM is Iron ion inside this protein. I do not know which >> forcefield is >> > >>>>> proper to use. I also tried MARTINI force field according their >> website; I >> > >>>>> used martinize.py script; Again I got error. >> > >>>>> >> > >>>>> Regards, >> > >>>>> Dariush >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul >> wrote: >> > >>>>> >> > >>>>>> >> > >>>>>> Dariush Mohammadyani wrote: >> > >>>>>> >> > >>>>>>> Hi all, >> > >>>>>>> >> > >>>>>>> Has a
Re: [gmx-users] Cytochrom C
Dear Justin, I could not find HIS in CHARMM and GROMOS53a6. Somebodies offer to rename it to HSE or HSD, but I do not know why? and which one is correct. I am working on Cytochorom c. Thanks, Dariush On Tue, Jan 10, 2012 at 4:22 PM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> Does anybody know where can I find [ HIS ] parameters? >> >> > HIS is histidine; it's built into every one of the force fields in Gromacs. > > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Coarse Grained Cytochrom C
Hi all, Has anybody used Coarse grained model for Cytochrome C? I could create a model using MARTINI forcefiels (using martinize.py script and 1HRC.pdb file), but it does not have HEM and HOH groups. Can anybody help me? Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Cytochrom C
According your help and "pdb2gmx -his -missing" I could create input files. Also I used grompp without error. However, for mdrun I got this error: *Function type CMAP Dih. not implemented in ip_pert* How can I figure it out? Thanks, Dariush On Tue, Jan 10, 2012 at 4:37 PM, Krzysztof Kuczera wrote: > Hi Dariush > If you are using the CHARMM27 force field, then all topology and parameters > are in your share/top/charmm27.ff directory > The defined molecules are listed in aminoacids.rtp and force field > parameters in > numerous other files. CHARMM does not use 'HIS' for histidine, but has > HSD, HSE and HSP for the isomers with hydrogen at ND1, NE2 and both. > You can either set these isomers by hand - by editing your PDB file or use > the > 'pdb2gmx -his' option for interactive definition. > > The bonus of keeping 'HIS' names and interactive setup is that bonds to > heme > iron will be generated based on the 'specbond.dat' entries, if HIS NE2 > nitrogens are close enough to the FE. > > Krzysztof > > > > On 1/10/12 2:40 PM, Dariush Mohammadyani wrote: > > Does anybody know where can I find [ HIS ] parameters? > > Thanks, > Dariush > > > On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani < > d.mohammady...@gmail.com> wrote: > > Dear Peter and Krzyszto, > > Thank you. I am following your comments. If I get any problem I will come > back. > > > > > On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai wrote: > > He must be using an older version of Gromacs. 4.5.4 and lower don't have > ACE in charmm27. > > On 2012-01-06 12:59:56PM -0600, Krzysztof Kuczera wrote: > > Here is the blocking group from > > gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp > > KK > > > > [ ACE ] > > [ atoms ] > > CH3 CT3 -0.270 0 > > HH31HA 0.090 1 > > HH32HA 0.090 2 > > HH33HA 0.090 3 > > C C 0.510 4 > > O O -0.510 5 > > [ bonds ] > > C CH3 > > C +N > > CH3 HH31 > > CH3 HH32 > > CH3 HH33 > > O C > > [ impropers ] > > C CH3 +N O > > > > > > On 1/6/12 12:40 PM, Peter C. Lai wrote: > > > Corrected bonds section (sorry been up all night) > > > > > > [ ACE ] > > >[ atoms ] > > > CH3CT3-0.270 > > > HH31 HA 0.091 > > > HH32 HA 0.092 > > > HH33 HA 0.093 > > > CC 0.514 > > > OO -0.515 > > > [ bonds ] > > > CH3HH31 > > > CH3HH32 > > > CH3HH33 > > > CH3C > > > C O > > > > > > Surprisingly, an .hdb entry for ACE exists so you don't need to > create one. > > > (and the .hdb entry uses HH3 as the base hydrogen name in ACE) > > > > > >> > > >> On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote: > > >>> Gromos96 53A6 has it. > > >>> > > >>> On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote: > > >>>> I tried charmm27 too. > > >>>> > > >>>> Error: > > >>>> Residue 'ACE' not found in residue topology database > > >>>> > > >>>> I tried all forcefield in the list provided by "pdb2gmx", but non > of them > > >>>> works. > > >>>> > > >>>> Dariush > > >>>> > > >>>> > > >>>> On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers > wrote: > > >>>> > > >>>>> HEME is in the charmm27 force field. > > >>>>> bob h. > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>> On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: > > >>>>> > > >>>>> Yes, I have PDB file (1HRC.pdb). However, when I try to use > "pdb2gmx" I > > >>>>> get this error: > > >>>>> > > >>>>> Residue 'HEM' not found in residue topology database > > >>>>> > > >>>>> and HEM is Iron ion inside this protein. I do not know which > forcefi
Re: [gmx-users] Cytochrom C
Dear Justin, You are right, I had some warning and with -missing I override them, e.g.: WARNING: atom HA is missing in residue HEM 105 in the pdb file WARNING: atom HB is missing in residue HEM 105 in the pdb file ... 30 missing atoms. I did not know how should figure them out. I am using GROMACS 4.5.3 and charmm27.ff. Cytochrome C is a difficult protein to simulate :( Thanks, Dariush On Tue, Jan 17, 2012 at 10:33 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> According your help and "pdb2gmx -his -missing" I could create input >> files. Also I used grompp without error. However, for mdrun I got this >> error: >> > > Using the -missing flag is very dangerous. If you're using it to override > warnings or errors that pdb2gmx is giving, your simulations will almost > certainly be junk because the topology is broken. > > *Function type CMAP Dih. not implemented in ip_pert* >> >> >> How can I figure it out? >> >> > Without seeing your .mdp file and knowing which Gromacs version you're > using, there's little anyone can do to help you. The error suggests you're > trying to transform a CMAP dihedral using the free energy code, which > cannot be done (per the error message). > > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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] NAMD file (.inp) convert to GROMACS format
Hi all, I have two files (Topology and Parameter files) in NAMD format (*.inp). I am going to use them in GROMACS. Can you help me how can I use them? Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] NAMD file (.inp) convert to GROMACS format
Is there any similar script to change it for this reason? On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> Hi all, >> >> I have two files (Topology and Parameter files) in NAMD format (*.inp). I >> am going to use them in GROMACS. >> Can you help me how can I use them? >> >> > You'll have to have a good working knowledge of all file formats involved > (which, for Gromacs, requires a thorough read through Chapter 5 of the > manual) and design a script that will parse the relevant information from > your existing files and write them into Gromacs format. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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] NAMD file (.inp) convert to GROMACS format
Thanks Justin! There is one script in User Contributions page, but it does not work. I totally changed my way, I will use NAMD in this case... On Fri, Jan 27, 2012 at 2:11 PM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> Is there any similar script to change it for this reason? >> >> > If there is one that exists, it may have been posted to the User > Contributions page of the Gromacs website. If not, maybe someone will post > one for you. > > I've seen this question asked before with no answer, so likely it's time > to break out the NAMD and Gromacs manuals in concert with your favorite > text editor and scripting language, and have at it. > > -Justin > > >> On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Dariush Mohammadyani wrote: >> >>Hi all, >> >>I have two files (Topology and Parameter files) in NAMD format >>(*.inp). I am going to use them in GROMACS. >>Can you help me how can I use them? >> >> >>You'll have to have a good working knowledge of all file formats >>involved (which, for Gromacs, requires a thorough read through >>Chapter 5 of the manual) and design a script that will parse the >>relevant information from your existing files and write them into >>Gromacs format. >> >>-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://vt.edu/Pages/Personal/justin> >> >> <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> >> >> >> <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> >> >> >> <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-request@**gromacs.org >> >. >>Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> >> > -- > ==**== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] Martini
SC5 does not work? Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Thu, Mar 8, 2012 at 2:34 PM, dina dusti wrote: > Dear Gromacs Specialists, > > May I ask you to help me for definition of pyrrole, tiofen and aniline in > MARTINI coarse-grained force field, Please? > I defined them as following: > aniline (one benzene ring+NH2) = SC4, SC4, SNd > pyrrole (one aromatic ring consists of 4 carbon and one NH) = SC4, SP1 > tiofen (one aromatic ring consists of 4 carbon and one S) = ??? > May I ask you to tell me your idea about these molecules, Please? > > Thank you in advance. > Best Regards > Dina > > > -- > 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] Martini
I think I made a mistake: Aniline: SC4 -SC4 - SNd Pyrrole: SC4 -SNd Tiofen: SC4 - SC5 I am not sure... On Thu, Mar 8, 2012 at 3:24 PM, dina dusti wrote: > Dear Dariush, > > Thank you very much from your response. > Then you tell me that the definition of aniline and pyrrole, is correct? > Is your mean about SC5 for tiofen means that it is defined as SC4 and SC5 > for tiofen? indeed I had doubt about this definition because S is without H > in tiofen. > May I know your cause for this definition, Please? > > Best Regards > Dina > ------ > *From:* Dariush Mohammadyani > *To:* dina dusti ; Discussion list for GROMACS users > > *Sent:* Thursday, March 8, 2012 11:24 PM > *Subject:* Re: [gmx-users] Martini > > SC5 does not work? > Dariush > > -- > Kind Regards, > Dariush Mohammadyani > Department of Structural Biology > University of Pittsburgh School of Medicine > Biomedical Science Tower 3 > 3501 Fifth Avenue > Pittsburgh, PA 15261 > USA > > > > On Thu, Mar 8, 2012 at 2:34 PM, dina dusti wrote: > > Dear Gromacs Specialists, > > May I ask you to help me for definition of pyrrole, tiofen and aniline in > MARTINI coarse-grained force field, Please? > I defined them as following: > aniline (one benzene ring+NH2) = SC4, SC4, SNd > pyrrole (one aromatic ring consists of 4 carbon and one NH) = SC4, SP1 > tiofen (one aromatic ring consists of 4 carbon and one S) = ??? > May I ask you to tell me your idea about these molecules, Please? > > Thank you in advance. > Best Regards > Dina > > > -- > 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 > -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] clashes
Dear user, When I am using: genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro to add water in a coarse grained system, after running mdrun I am getting "Syntax error" and it shows maybe the distances are so close or there are some clashes. Do you know how can I figure it out? Or actually if we have some clashes in system how we can correct them? Thanks, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] clashes
Yes, you are right. I made a mistake to write an error: [n0017:07436] *** Process received signal *** [n0017:07436] Signal: Segmentation fault (11) [n0017:07436] Signal code: Address not mapped (1) [n0017:07436] Failing at address: 0x1d620d20 What do you mean for "Better energy minimization"? Thanks, Dariush On Wed, Mar 14, 2012 at 10:08 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> Dear user, >> When I am using: >> genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro >> to add water in a coarse grained system, after running mdrun I am >> getting "Syntax error" and it shows maybe the distances are so close or >> there are some clashes. >> >> > > I've never heard of mdrun throwing a syntax error. Can you please copy > and paste the complete error message from your terminal? > > > Do you know how can I figure it out? >> Or actually if we have some clashes in system how we can correct them? >> >> > > Better energy minimization typically solves bad atomic clashes. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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] Box Size in MD
As far as I concern, the minimum size is that cove all parts of your molecules or system. In case you should use solvent it is up to you to add how many molecules and in this case you should make decision by experience or according to literature. Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Thu, Mar 22, 2012 at 12:08 PM, Lara Bunte wrote: > Hello > > What size should a box have in that you do your MD? I always read that for > short Lennard Jones interactions one should do a cut off with the half of > the box size but what how to know a good box size? > > Thanks for help > Greetings > Lara > -- > 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] About Distance.pl script
I have gotten this error previously. I changed the address of the g_dist (e.g. /user/gromacs/bin/g_dist) in distances.pl file and it works. Dariush On Thu, Mar 29, 2012 at 11:51 AM, vidhya sankar wrote: > Dear justin , Thank you for your previous reply > When i Download and run Distance.pl script In your website I got the > following error > > > readline() on closed filehandle IN at ./Distance.pl line 16. > Use of uninitialized value $distance in concatenation (.) or string at > ./Distance.pl line 30. > > How to rectify this error ? > Thanks in Advance > With regards > S.Vidhyasankar > > -- > 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] Position Restraints
Dear All, I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid bilayer. Although I used: define = -DPOSRES components in system were moving around and interact with each other. Then, I cannot do NVT or NPT equilibration. Could you please let me know how can I control this kind of movements? Regards, Dariush -- 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] Position Restraints
Thanks dear Justin. No, the protein is moving in right direction, but I am going to restrain any changing the position and then monitory these movements during MD run. I could see the Pos. Res. works in md.log file. Regards, Dariush On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul wrote: > > > On 4/26/12 1:35 PM, Dariush Mohammadyani wrote: > >> Dear All, >> I am using CG-MD using MARTINI forcefield. The system contains Protein >> and lipid >> bilayer. Although I used: >> define = -DPOSRES >> components in system were moving around and interact with each other. >> Then, I >> cannot do NVT or NPT equilibration. >> Could you please let me know how can I control this kind of movements? >> > > If molecules that should be restrained are moving inappropriately, then > the restraints are not being replied properly in the topology. In the > absence of more substantial information, there's nothing else that can be > said. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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] fly some lipids to water
Dear Users, I am simulation bilayer composed of 81 DOPC and 21 cardiolipin (CL) in a box size 6*6*20 (nm^3). For making this system I used DOPC system with a zero surface tension and then I replaced each DOPC with one CL. Now, I got strange result, after long run, some of lipid (most of them are cardiolipin) fly away from bilayer and come inside the water. Does anybody know what is the problem? How should I fix my system? I am using Coarse grained model using MARTINI force field. Thanks, Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- 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] MARTINI parameters for dodecyl maltoside (DDM)
Have you checked MARTINI website? http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters Dariush Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Sun, May 20, 2012 at 1:01 PM, francesco oteri wrote: > Dear gromacs users, > does someone of you know whether parameters for the detergent > dodecyl-beta-maltoside > are avalaible in MARTINI forcefield? > > Thank you in advance, > Francesco > > -- > 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] MARTINI parameters for dodecyl maltoside (DDM)
Sure, this is the way to make forcefield for your molecule. Also, please check literature. Good luck, Dariush On Mon, May 21, 2012 at 9:26 AM, francesco oteri wrote: > Hi Dariush, > I've checked but it seems there no parameters for my detergent. > > Actully there are parameters for the polar head and the lipidic tail, so > it is worth trying to merge them > to have the correct representation! > > Francesco > > 2012/5/21 Dariush Mohammadyani > >> Have you checked MARTINI website? >> http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters >> >> Dariush >> >> >> >> >> Kind Regards, >> Dariush Mohammadyani >> Department of Structural Biology >> University of Pittsburgh School of Medicine >> Biomedical Science Tower 3 >> 3501 Fifth Avenue >> Pittsburgh, PA 15261 >> USA >> >> >> >> On Sun, May 20, 2012 at 1:01 PM, francesco oteri < >> francesco.ot...@gmail.com> wrote: >> >>> Dear gromacs users, >>> does someone of you know whether parameters for the detergent >>> dodecyl-beta-maltoside >>> are avalaible in MARTINI forcefield? >>> >>> Thank you in advance, >>> Francesco >>> >>> -- >>> 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 >> > > > > -- > Cordiali saluti, Dr.Oteri Francesco > > -- > 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] Simple question (confout)
Hi, Is there any difference between confout.gro file and last frame which we can extract from trajectory? I am thinking they are different!! When I see the trajectory I can see the edge of the well-shaped box, but when I see confout.gro it is not well-shaped and some atoms looks went out out of the box. PS: It does not matter either NPT or NVT was used. Thanks, Dariush -- 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] Bilayer curvature
Dear All, I have set two bilayers: 1. 400 DOPC 2. 320DOPC and 80 Cardiolipin Second one show significant curvature during NPT equilibrium and MD run (not in NVT eq.). Is it normal? For the first bilayer, after adding the protein to the system, here also I can see big curvature in the membrane. Does anybody knows is it normal or something is wrong? Which factors do affect the membrane curvature (like: initial conf., water, ions, box size, equilibration steps, ...)? Thanks, Dariush -- 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
