Re: [gmx-users] DSSP regardin
Hi Rahul,
I've run into a similar issue a year ago. It is possible to configure gmx
with the extra configuration file (as described in the documentation) to
get this right.
However, I found it to be archaic and wrote my own quick DSSP visualiser in
matplotlib.
I am planning to improve the code and release it with the next paper, but
for now I attach the simple one.
Note that not all dssp letters/secondary structures have been added, so you
might need to add more colors:
colors = {
coil_char: "#FF",
bsheet_char: "#FF",
bbridge_char: "#00",
bend_char: "#008000",
turn_char: "#00",
three_helix_char: "#808080",
}
Hope this helps, Mat
On Fri, 15 Mar 2019 at 17:06, RAHUL SURESH wrote:
> Hi Users.
>
> I have Performed dssp for 1000ns simulation. On converting the xpm to eps,
> the axis are not visible to any extent. I have tried with different values
> and I couldn't obtain a good image. Can anyone pass possible suitable
> commands for long simulations to obtain a satisfactory image?
>
> --
> *Regards,*
> *Rahul *
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Re: [gmx-users] CU2+ nonbonded parameteres (sigma and epsilon)
On 3/16/19 9:06 AM, Mohsen Asadbegi wrote: Thanks for your answer, I want to simulate interaction of amyloid-beta peptide and CU(II) ion in non-bonded modes. Non-bonded parameters of some metal ions like ZN(II), CAD(II), and CA(II) are provided in CHARMM36. So what is the difference among copper ion and zinc/cadmium and calcium ions? Moreover, I the last version of CHARMM36, non-bonded parameters of the copper metal CU is added, but I need parameters of the CU(II) ion. Pairwise-additive force fields do not treat transition metals well. There are some approximate parameter sets, including a full set of parameters that are purportedly compatible with CHARMM (e.g. dx.doi.org/10.1021/jp309150r) but they do require additional refinement in the context of protein interactions. In short, trying to derive any useful information in terms of ion comparisons in systems like these is beyond the current capabilities of classical, nonpolarizable MD simulations. QM/MM is the way to go (and there are numerous studies already published that have done what you're seeking to do). As Paul said, there are physical properties that MD force fields cannot describe, which have profound impact on the properties that are critical to the comparison you seek to do, not the least of which would be charge transfer and coordination geometry. A sphere with +2 charge will never get those things right. -Justin Regards Mohsen On Sat, 16 Mar 2019 at 16:28, Paul Bauer wrote: Hello, Classical force fields are a bad way to describe the behaviour of transition metals such as CU2+, because they are not able to cover the behaviour of the D-orbitals with just the sigma and epsilon parameters. What are you planning to use the model for? It is possible to parametrize transition metals for this, but it is a lengthy and time consuming process. Kindest regards Paul On Fri, 15 Mar 2019, 19:53 Mohsen Asadbegi, wrote: Hi! I need to add non-bonded CU2+ ion to CHRAMM36. How can I find these parameters (sigma and epsilon)? Does it enough to define CU2+ by its charge, mass, sigma and epsilon? In addition, I want to know that what are the units of sigma and epsilon in the CHARMM36 force field? Regards, Mohsen Asadbegi. -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] CU2+ nonbonded parameteres (sigma and epsilon)
Thanks for your answer, I want to simulate interaction of amyloid-beta peptide and CU(II) ion in non-bonded modes. Non-bonded parameters of some metal ions like ZN(II), CAD(II), and CA(II) are provided in CHARMM36. So what is the difference among copper ion and zinc/cadmium and calcium ions? Moreover, I the last version of CHARMM36, non-bonded parameters of the copper metal CU is added, but I need parameters of the CU(II) ion. Regards Mohsen On Sat, 16 Mar 2019 at 16:28, Paul Bauer wrote: > Hello, > > Classical force fields are a bad way to describe the behaviour of > transition metals such as CU2+, because they are not able to cover the > behaviour of the D-orbitals with just the sigma and epsilon parameters. > What are you planning to use the model for? It is possible to parametrize > transition metals for this, but it is a lengthy and time consuming process. > > Kindest regards > Paul > > On Fri, 15 Mar 2019, 19:53 Mohsen Asadbegi, > wrote: > > > Hi! > > > > I need to add non-bonded CU2+ ion to CHRAMM36. How can I find these > > parameters (sigma and epsilon)? Does it enough to define CU2+ by its > > charge, mass, sigma and epsilon? > > In addition, I want to know that what are the units of sigma and epsilon > in > > the CHARMM36 force field? > > > > Regards, > > Mohsen Asadbegi. > > -- > > 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. > -- 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] CU2+ nonbonded parameteres (sigma and epsilon)
Hello, Classical force fields are a bad way to describe the behaviour of transition metals such as CU2+, because they are not able to cover the behaviour of the D-orbitals with just the sigma and epsilon parameters. What are you planning to use the model for? It is possible to parametrize transition metals for this, but it is a lengthy and time consuming process. Kindest regards Paul On Fri, 15 Mar 2019, 19:53 Mohsen Asadbegi, wrote: > Hi! > > I need to add non-bonded CU2+ ion to CHRAMM36. How can I find these > parameters (sigma and epsilon)? Does it enough to define CU2+ by its > charge, mass, sigma and epsilon? > In addition, I want to know that what are the units of sigma and epsilon in > the CHARMM36 force field? > > Regards, > Mohsen Asadbegi. > -- > 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] Replica exchange MD analysis
Dear Friends, I performed REMD by following tutorial provided by Mark Abraham, But I am not able to get the analysis part. Is a step-wise tutorial available ? I would be thankful to you if anyone of you could help me to perform analysis of REMD output. Thanking you Regards RajP -- 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] (no subject)
Dear all I encountered with following error when running the umbrella sampling simulation of a protein. What modification should I make in the pull code to get rid of the error. ERROR 1 [file npt_umbrella.mdp]: When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbcatom. Pull group 1 is larger than that and does not have a specific atom selected as reference atom. Pull group natoms pbc atom distance at start reference at t=0 1 226 113 2 226 339 1.396 nm 1.396 nm Estimate for the relative computational load of the PME mesh part: 0.14 This run will generate roughly 13 Mb of data Thanks in advance -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- 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.
