[gmx-users] Adding ions
Hi GROMACS users, I solved my proteinin a defined box of water. Now I want to add ions to neutralize thesystem. But when I use “grompp -f ions.mdp -c solv.gro -pgromacs.top -o ions.tpr” to generate the .tpr file I receive thiserror : Fatal error:No such moleculetypeSOLFor more informationand tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors in the .gro and .topboth the SOL exists. I don not know what the problem is exactly.Also, before thiscommand I defined the box and solved the proteins by these commands: gmx editconf -fgromacs.gro -o protein.gro -c -box 8gmx solvate -cpprotein.gro -cs spc216.gro -o solv.gro -p gromacs.top Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] QM calculation
Thank you very much Justin for your helpful answer. On Thursday, March 31, 2016 3:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 3/31/16 12:19 AM, mohammad r wrote: > Thank you Justin, I want to do QM calculationbefore running equilibration > then run the MD simulation by GROMACS. Do you knowwhich software is > appropriate and compatible with GROMACS that after QM calculation I can run > the rest of simulation? Again, for a pure QM calculation (geometry optimization, I presume) there is no interaction with GROMACS or any other software. You do your optimization, output the coordinates, and then move on. If I'm missing some critical detail, please describe exactly what you want to do. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] QM calculation
Thank you Justin, I want to do QM calculationbefore running equilibration then run the MD simulation by GROMACS. Do you knowwhich software is appropriate and compatible with GROMACS that after QM calculation I can run the rest of simulation? Best, Mohammad. On Thursday, March 31, 2016 3:43 AM, Justin Lemkul <jalem...@vt.edu> wrote: On 3/30/16 2:17 AM, mohammad r wrote: > Hi gromacs users, > > > > I want to do QMcalculation to my system. Can the PRODRG sitedo it (according > to gromacs tutorial)? Or I should do it by using gromacsitself? By the way QM calculations are not reliant on MM topologies, like those from PRODRG (which are poor quality anyway) or any force field terms. GROMACS does not do QM directly, though there are interfaces to popular QM codes for doing QM/MM. For strict QM, abandon GROMACS and use the appropriate software. > I’ve generated the initial coordinate and topology files inamber tools then > convert it to gromacs format by using parmed (because theforce field which I > want is not included in gromacs). > Again, for a pure QM calculation, there is no need for any MM programs or force fields. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] QM calculation
Hi gromacs users, I want to do QMcalculation to my system. Can the PRODRG sitedo it (according to gromacs tutorial)? Or I should do it by using gromacsitself? By the way I’ve generated the initial coordinate and topology files inamber tools then convert it to gromacs format by using parmed (because theforce field which I want is not included in gromacs). Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Neutralizing
Thank you Justin for your help. On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 3/9/16 1:42 AM, mohammad r wrote: > Thank you Parham and Justin, Excuse me I have another question, in simulation > of a water-peptide system, is it necessary to use QM/MM simulation during the > entire process? Because I didn't see it in the tutorials. By the way I > generated the pdb file by using charmm-gui then import it in amber to get the > topology and coordinate files, finally I converted the topology and > coordinate files to gromacs format and did the rest of simulation by gromacs. > but I didn't run QM/MM simulation. Does it make trouble in the results? The technique(s) used depend on the scientific question(s) being posed before doing the simulations. If you expect some reactions, etc. to be taking place, then you need QM/MM. If you just want to simulate a peptide over time, then plain MD is fine. Methodological details like this should be decided long before one approaches a keyboard :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Neutralizing
Thank you Parham and Justin, Excuse me I have another question, in simulation of a water-peptide system, is it necessary to use QM/MM simulation during the entire process? Because I didn't see it in the tutorials. By the way I generated the pdb file by using charmm-gui then import it in amber to get the topology and coordinate files, finally I converted the topology and coordinate files to gromacs format and did the rest of simulation by gromacs. but I didn't run QM/MM simulation. Does it make trouble in the results? Best, Mohammad. On Wednesday, March 9, 2016 4:26 AM, Justin Lemkul <jalem...@vt.edu> wrote: On 3/8/16 3:59 AM, mohammad r wrote: > Thank you Parham > You mean that it is not necessary to do QM/MM simulation? > The trivial task of adding ions to neutralize the net charge on the system certainly does not require anything like QM/MM. -Justin > On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of >Biomedical Science) <pjabbarza...@gmail.com> wrote: > > > Dear Sir > > Use this command: > > gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral > > In this case, you don't need the number of ions. > Kind Regards > > Parham J. K. > ===== > PhD candidate - Lecturer in drug discovery > Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia > =====Publication ::: Featured Publication ::: Website > ::: FaceBook > On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0...@yahoo.com> wrote: > > Hi everybody, I’ve generated a water-peptide system, now I want to neutralize > it. Is adding adequate number of ions sufficient for neutralizing process or > I should do QM/MM simulation for the this process? Thank you, Mohammad. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > > > > > -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Neutralizing
Thank you Parham You mean that it is not necessary to do QM/MM simulation? On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of Biomedical Science) <pjabbarza...@gmail.com> wrote: Dear Sir Use this command: gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral In this case, you don't need the number of ions. Kind Regards Parham J. K. ===== PhD candidate - Lecturer in drug discovery Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia =====Publication ::: Featured Publication ::: Website ::: FaceBook On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0...@yahoo.com> wrote: Hi everybody, I’ve generated a water-peptide system, now I want to neutralize it. Is adding adequate number of ions sufficient for neutralizing process or I should do QM/MM simulation for the this process? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Neutralizing
Hi everybody, I’ve generated a water-peptide system, now I want to neutralize it. Is adding adequate number of ions sufficient for neutralizing process or I should do QM/MM simulation for the this process? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] modeling CNT, center of mass velocity, energy minimization
Hi GROMACS users, I have some questions: 1- Can I model a carbonnanotube (CNT) conveying fluid in GROMACS subjected to a magnetic field?2- How can I check the centerof mass velocity of my system?3- I want to calculate volumeand water self diffusion coefficient for 1ns, can the energy minimizationprocess do it? Or the equilibrium processes can do it? I want to draw theparameters versus time. Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] modeling CNT, center of mass velocity, energy minimization
Hi GROMACS users, I have some questions: 1- Can I model a carbonnanotube (CNT) conveying fluid in GROMACS subjected to a magnetic field? 2- How can I check the centerof mass velocity of my system? 3- I want to calculate volumeand water self diffusion coefficient for 1ns, can the energy minimizationprocess do it? Or the equilibrium processes can do it? I want to draw theparameters versus time. Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Potential energy
Thank you Justin, do you know how I can find or modify the center of mass velocity of my system? On Sunday, February 21, 2016 11:50 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 2/21/16 3:15 PM, mohammad r wrote: > Hi everybody, > > > > Is it correct to say the potential energy after energyminimization should be > negative and in the order of 105-106 ?according to gromacs tutorial: > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html > As a broad generalization, but strictly speaking, that's not always true. A comparable protein in a similarly sized box will probably have something on that order, but that is by no means an absolute rule. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Potential energy
Hi everybody, Is it correct to say the potential energy after energyminimization should be negative and in the order of 105-106 ?according to gromacs tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] converted topology from amber to gromacs
Thank you very much Justin
On Saturday, February 20, 2016 10:53 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 2/20/16 8:49 AM, mohammad r wrote:
> Hi Justin,
>
> Thank you for your answer, I used grompp and it didn't give me error. I've
> attached a topology file of my systems. Can you please take a look at this and
> tell me your opinion? You mean that it doesn't make any problem when after
> conversion process the topology file doesn't refer to any force field?
>
The topology lists all needed parameters explicitly. Note the header that says
"This is a standalone topology." "Standalone" means "I have everything you
need
right here."
The purpose of the #include function in GROMACS is to say "copy and paste the
contents of the file here." That is the same thing for grompp as listing all
parameters explicitly.
There is no problem here with your topology. It just looks a little different,
but if you understand a little bit about how GROMACS assembles topologies, it
becomes obvious that this is a slightly more verbose version of what you are
used to seeing.
-Justin
> Thank you, Mohammad.
>
>
>
>
> On Friday, February 19, 2016 4:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
>
>
> On 2/19/16 3:26 AM, mohammad r wrote:
> >
> > I don't know whether the problem is with the converting process (gromacs
> topology file doesn't refer to any force filed) or the the process of
> generating
> files in amber tools is wrong.
> >
>
> Are you getting some specific problem in GROMACS? ParmEd should give you a
> self-contained topology file that explicitly lists the parameters it uses. It
> may not fit the convention of the normal sequence of #include statements
> because
> it's using a slightly different, but equally valid, approach.
>
> Without seeing your topology, it's impossible to figure out if there is any
> problem. grompp is the quickest test here. If it doesn't complain, you're
> fine.
>
> -Justin
>
> > On Friday, February 19, 2016 11:04 AM, mohammad r
> <mohammad.r0...@yahoo.com <mailto:mohammad.r0...@yahoo.com>> wrote:
> >
> >
> > #yiv7024757511 p
> {margin-bottom:0.1in;direction:ltr;line-height:120%;text-align:justify;}#yiv7024757511
> p.yiv7024757511western {font-size:12pt;}#yiv7024757511 p.yiv7024757511cjk
> {font-size:12pt;}#yiv7024757511 p.yiv7024757511ctl {font-size:12pt;}I used
> ff14SBAmber protein force field, #yiv7024757511 p
> {margin-bottom:0.1in;direction:ltr;line-height:120%;text-align:justify;}#yiv7024757511
> p.yiv7024757511western {font-size:12pt;}#yiv7024757511 p.yiv7024757511cjk
> {font-size:12pt;}#yiv7024757511 p.yiv7024757511ctl {font-size:12pt;}
> LIPID11force field and TIP3P water model. First I loaded the force fields and
> water model then loaded the pdb file and finally I saved the topology and
> coordinate files.
>
> >
> >
> > On Friday, February 19, 2016 10:40 AM, Hai Nguyen <nhai...@gmail.com
> <mailto:nhai...@gmail.com>> wrote:
> >
> >
> > Hi
> > You should know which AMBER force field when you made the topology file.
>(How
> did you make it?)
> > Hai
> > On Fri, Feb 19, 2016 at 12:56 AM, mohammad r <mohammad.r0...@yahoo.com
> <mailto:mohammad.r0...@yahoo.com>> wrote:
> >
> > Hi gromacs users,
> > I've generatedinitial structure of my system by using ambertools (topology
> andcoordinate files) and converted it to gromacs format (.gro and .top)by
> parmed, but in topology file it doesn't refer to any forcefield.Does it make
> any
> problem in the results or it is ok? Because when Icompare the simulation
> result
> with experiment it is incorrect.
> > Thank you, Mohammad.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List>before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>or send a
> mail to gmx-users-requ...@gromacs.org. <mailto:gmx-users-requ...@gromacs.org.>
>
> >
> >
> >
> >
> >
> >
> >
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Healt
[gmx-users] converted topology from amber to gromacs
Hi gromacs users, I've generatedinitial structure of my system by using ambertools (topology andcoordinate files) and converted it to gromacs format (.gro and .top)by parmed, but in topology file it doesn't refer to any forcefield.Does it make any problem in the results or it is ok? Because when Icompare the simulation result with experiment it is incorrect. Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] DSSP secondary structure
Thank you Justin, I did it by using xpm2ps and ps2pdf commands. Now I want to ask, is there any way to calculate the percentage of a-helical structure of a protein during simulation? Indeed DSSP visualize it but I want to calculate it exactly. Thanks, Mohammad. On Monday, February 15, 2016 6:31 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 2/15/16 1:31 AM, mohammad r wrote: > I changed and reduced the ratio but the xpm file was not changed at all. > Unfortunately there's not much I can tell you here because this is rather cryptic. It's illogical to get the same output with different input. You can calculate exactly what values to use based on the number of residues in the protein (y-axis) and number of frames (x-axis). Then scale xbox accordingly to fit some nicely shaped rectangle of defined proportions. -Justin > > On Sunday, February 14, 2016 5:05 PM, Justin Lemkul <jalem...@vt.edu> >wrote: > > > > > On 2/14/16 1:54 AM, mohammad r wrote: >> Thank you Justin, >> >> I used xpm2ps command with below m2p file but the resolution was not changed. >> I've attached the xpm file, even the legend can't be seen. >> is there anyway to get the result file in pdf format? >> >> m2p file (I found it in the gromacs website): >> > >> xbox = 2.0 ; x‐size of a matrix element >> ybox = 2.0 ; y‐size of a matrix element > > You have a rectangular matrix, with the x-dimension being much longer than the > y-dimension. If you set these two values to be the same, what happens to the > size of the rectangle? It gets uniformly scaled. So naturally that > accomplishes nothing. What you need to do is reduce the ratio of xbox/ybox. > > -Justin > -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] DSSP secondary structure
I changed and reduced the ratio but the xpm file was not changed at all. On Sunday, February 14, 2016 5:05 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 2/14/16 1:54 AM, mohammad r wrote: > Thank you Justin, > > I used xpm2ps command with below m2p file but the resolution was not changed. > I've attached the xpm file, even the legend can't be seen. > is there anyway to get the result file in pdf format? > > m2p file (I found it in the gromacs website): > > xbox = 2.0 ; x‐size of a matrix element > ybox = 2.0 ; y‐size of a matrix element You have a rectangular matrix, with the x-dimension being much longer than the y-dimension. If you set these two values to be the same, what happens to the size of the rectangle? It gets uniformly scaled. So naturally that accomplishes nothing. What you need to do is reduce the ratio of xbox/ybox. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] DSSP secondary structure
Thank you Justin, I used xpm2ps command with below m2p file but the resolution was not changed. I've attached the xpm file, even the legend can't be seen.is there anyway to get the result file in pdf format? m2p file (I found it in the gromacs website): black = no ; Obsoletetitlefont = Times‐Roman ; A PostScript Fonttitlefontsize = 20 ; Font size (pt)legend = yes ; Show the legendlegendfont = Times‐Roman ; A PostScript Fontlegendlabel = ; Used when there is none in the .xpmlegend2label = ; Used when merging two xpm'slegendfontsize = 14 ; Font size (pt)xbox = 2.0 ; x‐size of a matrix elementybox = 2.0 ; y‐size of a matrix elementmatrixspacing = 20.0 ; Space between 2 matricesxoffset = 0.0 ; Between matrix and bounding boxyoffset = 0.0 ; Between matrix and bounding boxx‐major = 20 ; Major ticks on x axis every .. framesx‐minor = 5 ; Id. Minor ticksx‐firstmajor = 0 ; First frame for major tickx‐majorat0 = no ; Major tick at first framex‐majorticklen = 8.0 ; x‐majorticklengthx‐minorticklen = 4.0 ; x‐minorticklengthx‐label = ; Used when there is none in the .xpmx‐fontsize = 16 ; Font size (pt)x‐font = Times‐Roman ; A PostScript Fontx‐tickfontsize = 10 ; Font size (pt)x‐tickfont = Helvetica ; A PostScript Fonty‐major = 20y‐minor = 5y‐firstmajor = 0y‐majorat0 = noy‐majorticklen = 8.0y‐minorticklen = 4.0y‐label =y‐fontsize = 16y‐font = Times‐Romany‐tickfontsize = 10y‐tickfont = Helvetica On Saturday, February 13, 2016 9:44 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 2/13/16 1:33 AM, mohammad r wrote: > Hi, > I used the "gmx do_dssp" command to get the secondary structure of the > protein during the simulation but the resolution of the resulted .xpm file is > very low. how can I increase its resolution? You can adjust the matrix proportions with an .m2p file passed to xpm2ps -di. These are almost always necessary as there are many more frames than residues in the protein, usually an order of magnitude or more. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] DSSP secondary structure
Hi, I used the "gmx do_dssp" command to get the secondary structure of the protein during the simulation but the resolution of the resulted .xpm file is very low. how can I increase its resolution? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] DMF molecule
Hi everybody, I have the DMF pdb file and I want to import it to gromacs by pdb2gmx command, but the residues are not included in none of the forcefields. can you please help me figure this out? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] convert amber files to gromacs
Hi everybody, I want to convert the topology and coordinate files fromamber to gromacs format. I used acpype bu it didn’t work properly (actually mysystem is consisted of some lipids in a water-protein system but when I convertthe files via acpype, the backbone is consisted of a mass solvated in water,indeed in the converted topology file in the molecule types section the proteinand lipids assumed to be one mass and two molecule types exist: the water andthat mass), also I downloaded the “ambconv.tgz” from gromacs website but I don’tknow how to work with that. Can you please help me how to conver my files? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] installing gromacs-5.0.5
Hello everybody; I want to install gromacs-5.0.5 in ubuntu-14.04 using the installation instruction in the website "gromacs.org", but in the "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON" line I got this error: -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:160 (message): Cannot find compiler flags for 128 bit AVX with FMA support. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:720 (gmx_test_simd) -- Configuring incomplete, errors occurred! I've updated the gcc compiler but again this error occurred. I used the "sudo apt-get install gromacs" command but this installed the gromacs-4.6.5 and I want gromacs-5.0.5.can you help me, please? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] installing GROMACS
Hi; I tried to install GROMACS using "Installation guide for GROMACS 5.0.5" in the gromacs.org, but I got an error after typing "cmake .. " line, then I tried "sudo apt-get install gromacs" command, it installed the gromacs-4.6.5 but I want the gromacs-5.0.5. what should I do? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] adding lipids
Hi everybody; I have a cubic box with a peptide in its center (the .gro file). Now I want to add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of the lipid) to this box. But I don't know how to do it.I think that "gmx insert-molecules" command will help, but again I don't know how to use it, which parameters are needed. Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] adding lipids
Hi everybody; I have a cubic box with a peptide in its center (the .gro file). Now I want to add some lipids (e.g. 3 molecules)(I have the .gro and .top and .pdb files of the lipid) to this box. But I don't know how to do it.I think that "gmx insert-molecules" command will help, but again I don't know how to use it, which parameters are needed. Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] atom types IP and IM
Hi; I've used ff14sbamber force field to generate my system. As this force field doesn'texist in gromacs, I generated the first structure of my system withamber tools then I converted the topology and coordinate files intogromacs format by using acpype. (In the amber tools I've added NaClto my system). Now in the converted topology file I have these lines: [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; id_ at typeres nr residu name at name cg nr charge mass 1 IP 1 NA+ NA+ 1 1 22.9898 [ moleculetype ] ; molname nrexcl CL- 1 [ atoms ] ; id_ at typeres nr residu name at name cg nr charge mass 1 IM 1 CL- CL- 1 -1 35.45300 As we can see, wehave IP and IM atom types for Na+ and Cl- ions respectively. When Iwant to run energy minimization with the grompp command I get thiserror: Fatal error: Atomtype IP not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I think that itcannot recognize IP atom type. What should I do? Thank you, Mohammad -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353 Fatal error:Atomtype IP notfoundFor more informationand tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors I think that itcannot recognize the atoms. I don't know how to fix it. Best regards, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353 Fatal error:Atomtype IP notfoundFor more informationand tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors I think that itcannot recognize the atoms. I don't know how to fix it. Best regards, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353 Fatal error:Atomtype IP notfoundFor more informationand tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors I think that itcannot recognize the atoms. I don't know how to fix it. Best regards, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Hi;I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353 Fatal error:Atomtype IP notfoundFor more informationand tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors I think that itcannot recognize the atoms. I don't know how to fix it. Best regards, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] add NaCl
Hi; I've already converted topology and coordinate files which were generated with amber tools to .gro format. But now, when I want to add 100Mm NaCl to the system I get this error: Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'c6m1_GMX.top' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I think that it cannot recognize the solvent. How can I fix it? Thank you, Mohammad -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] acpype problem
Hi; I want to convert amber topology and coordinate files into gromacs topology and coordinate file with the acpype command ( acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd ), but when I type it, I get this error: acpype: command not found I've done the procedure mentioned in the website: https://code.google.com/p/acpype/wiki/HowToUse. I've downloaded the acpype with svn checkout http://acpype.googlecode.com/svn/trunk/ acpype command. I installed it with sudo ln -s $PWD/acpype.py /usr/local/bin/acpype command. but when I try to use acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd command, the error appeared . Thankyou, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] force field
Hi; I want to use ff14SB Amberprotein force field. But it isn't included in the gromacs force fields list.Is it possible to use this force field? How can I add it in?Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] force field
Thank you MaryamI want to use this force field in the first step of generating the topology file (pdb2gmx command in the force field shown after this command). Is it possible? and unfortunately I don't know how to find the necessary files of this force field. I searched a lot but I didn't succeed. I have another question, is it possible to acetylate or ammoniate a peptide with gromacs? thank you, M. On Sunday, August 9, 2015 8:17 PM, Maryam Kowsar maryam.kow...@gmail.com wrote: let me modify my previous message: in the g_x2top command, not grompp :-) On Sun, Aug 9, 2015 at 8:14 PM, Maryam Kowsar maryam.kow...@gmail.com wrote: Hi Mohammad, Yes that's possible. You should just have the necessary files of your desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp command just add -ff folder name. that's all! It will use your forcefield instead of the present forcefields in gromacs. Regards,-Maryam On Sun, Aug 9, 2015 at 5:57 PM, mohammad r mohammad.r0...@yahoo.com wrote: Hi; I want to use ff14SB Amberprotein force field. But it isn't included in the gromacs force fields list.Is it possible to use this force field? How can I add it in?Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
