Re: [gmx-users] [gmx-user] Autodock Vina Out use in gromacs MD

know if you think the given interactions are enough to keep the molecule at binding site for like 100ns? Thank you in Advance! Kind Regards Q On Tue, Dec 31, 2019 at 9:21 AM Justin Lemkul wrote: > > > On 12/30/19 1:51 PM, Quin K wrote: > > Further to following email, is it OK

Re: [gmx-users] [gmx-user] coordinates mismatch error

Thanks you!! I had forgotten to include the ligand atoms in the .gro file. I was able to correct the error! *Wishing you are Happy 2020~!* Thanks for all the help!! On Tue, Dec 31, 2019 at 9:15 PM Justin Lemkul wrote: > > > On 12/31/19 9:43 AM, Quin K wrote: > > Could it be

Re: [gmx-users] [gmx-user] coordinates mismatch error

Could it be due to protein-ligand complex being at the edge of the box? https://drive.google.com/file/d/187fPACfq1QybNJxkyJKB8faUPOBRFccK/view?usp=sharing On Tue, Dec 31, 2019 at 8:06 PM Quin K wrote: > Hi > > I continue to get following error during complex MD > > > > *

[gmx-users] [gmx-user] coordinates mismatch error

Hi I continue to get following error during complex MD *number of coordinates in coordinate file (solv.gro, 50670)does not match topology (topol.top, 50701)* I don't understand why there's a mismatch. I followed the instructions in mdtutorials.com for Gromacs ligand-protien complex. How can I

Re: [gmx-users] [gmx-user] Autodock Vina Out use in gromacs MD

, 2019 at 8:35 PM Quin K wrote: > Hi > > I noted when I used Autodock vina for docking and used the converted back > .mol2 file from .pdbqt format, there were a lot of changes in the molecule > than the molecule I initially submitted to Vina for docking. Like the *atomic > char

Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

Here are some details I gathered over some time and how I overcame the issue of *slow running gromacs* due to not using all threads in the intel processor. * Install according to following videos* https://www.youtube.com/watch?v=vOJsmtFeSGk https://www.youtube.com/watch?v=BZNzYt_DUB0 SIMD

[gmx-users] [gmx-user] Autodock Vina Out use in gromacs MD

Hi I noted when I used Autodock vina for docking and used the converted back .mol2 file from .pdbqt format, there were a lot of changes in the molecule than the molecule I initially submitted to Vina for docking. Like the *atomic charges were different. * Is this normal? or is there a way to use

[gmx-users] [gmx-user] 300K vs 310K for molecular dynamic simulation

Hi Which temperature should be used for molecular dynamic simulation of a human protein? If we used 300K would that give significantly different results from 310K MD simulation? Some argue that since human body temperature is around ~310K MD should be done at 310K. However I saw many papers that

Re: [gmx-users] [gmx-user] RMSD analysis of protein-ligand complex

Okay thank you! *What exactly should I do to fix the topology high penalty?* Do a DFT optimization again for the molecule and do the parametrization ? Is there a guideline to follow? On Thu, Dec 26, 2019 at 10:07 PM Justin Lemkul wrote: > On Thu, Dec 26, 2019 at 9:41 AM Quin K wr

Re: [gmx-users] [gmx-user] RMSD analysis of protein-ligand complex

, 2019 at 6:54 PM Justin Lemkul wrote: > > > On 12/26/19 9:05 AM, Quin K wrote: > > Thank you! > > This is the output I got from parachem. > > > https://docs.google.com/document/d/180rWUj4XE-_OFBCVPsJajohNRKUYIClcP_V3cOer5qw/view > > Can this be used as it is

Re: [gmx-users] [gmx-user] RMSD analysis of protein-ligand complex

during MD simulation? Thanks in advance! Regards Q On Wed, Dec 18, 2019 at 1:23 PM Justin Lemkul wrote: > > > On 12/18/19 6:40 AM, Quin K wrote: > > I generated ligand topology using parachem website, I didn't do any > > adjustments after, just used it as it is. > > What

Re: [gmx-users] [gmx-user] MD simulation of protein-ligand complex

simulation? On Tue, Dec 24, 2019 at 7:33 PM Justin Lemkul wrote: > > > On 12/24/19 12:47 PM, Quin K wrote: > > Hi > > Which of the following is the correct method to prepare a protein for > > docking and then for protein-ligand complex MD simulation? > > > > 1.

[gmx-users] [gmx-user] MD simulation of protein-ligand complex

Hi Which of the following is the correct method to prepare a protein for docking and then for protein-ligand complex MD simulation? 1. Do an MD simulation of protein for 100 ns and use the structure of protein at 100 ns to do the protein-ligand MD simulation. 2. Do an energy minimization of

Re: [gmx-users] [gmx-user] RMSD analysis of protein-ligand complex

I generated ligand topology using parachem website, I didn't do any adjustments after, just used it as it is. On Tue, 17 Dec 2019, 1:11 pm Justin Lemkul, wrote: > > > On 12/15/19 1:18 PM, Quin K wrote: > > Hi > > Thank you!!! > > > > Let's say during rest

Re: [gmx-users] [gmx-user] RMSD analysis of protein-ligand complex

ligand topology the only way to solve this issue? Thanks in advance. Regards On Sun, Dec 15, 2019 at 11:07 PM Justin Lemkul wrote: > > > On 12/15/19 11:47 AM, Quin K wrote: > > Hi All, > > > > Further to following email, i just noted that the ligand has detac

Re: [gmx-users] [gmx-user] RMSD analysis of protein-ligand complex

simulation? Your advice needed. Thank you in advance! On Sun, Dec 15, 2019 at 8:12 PM Quin K wrote: > Hi > > During RMSD analysis of protein ligand complex I got the following graph. > RMSD of how much the ligand position has varied relative to the protein is > given in the gr

[gmx-users] [gmx-user] RMSD analysis of protein-ligand complex

Hi During RMSD analysis of protein ligand complex I got the following graph. RMSD of how much the ligand position has varied relative to the protein is given in the graph (Please see the link below). https://drive.google.com/file/d/1rvkHYisjmjFDvN6Lldo5Gejz7nJKEKnl/view?usp=sharing I noted that

Re: [gmx-users] RMSD analysis of protein-ligand complex

Thank you Your advice is very helpful I will try to reparametrize the molecule, which I think is a better strategy. On Sun, Oct 6, 2019 at 6:38 AM Justin Lemkul wrote: > > > On 10/5/19 1:58 PM, Quin K wrote: > > Thank you. > > > > I examined the trajectory using VM

Re: [gmx-users] RMSD analysis of protein-ligand complex

(23ns) and I had to restart MD with append command. Could this have had an affect on MD? Do I have to recreate trajectory file after restarting MD, instead of using the default trajectory? Regards On Sat, Oct 5, 2019 at 9:53 PM Justin Lemkul wrote: > > > On 10/5/19 11:59 AM, Quin K wrote:

Re: [gmx-users] RMSD analysis of protein-ligand complex

Justin Lemkul wrote: > > > On 10/5/19 11:36 AM, Quin K wrote: > > OK thanks. > > What should I pick for least square fit in following instances for > example. > > *RMSD of* > > 1. protein backbone+ligand > > 2. protein backbone > > 3. lingad only > &

Re: [gmx-users] RMSD analysis of protein-ligand complex

OK thanks. What should I pick for least square fit in following instances for example. *RMSD of* 1. protein backbone+ligand 2. protein backbone 3. lingad only On Sat, Oct 5, 2019 at 8:56 PM Justin Lemkul wrote: > > > On 10/5/19 11:24 AM, Quin K wrote: > > Thank you! &g

Re: [gmx-users] RMSD analysis of protein-ligand complex

Thank you! How important is the least square fit in these RMSD calculations? Or should I just pick system for least square fit all time? On Sat, Oct 5, 2019 at 8:45 PM Justin Lemkul wrote: > > > On 10/5/19 11:11 AM, Quin K wrote: > > To see if complex is stable and to see h

Re: [gmx-users] RMSD analysis of protein-ligand complex

To see if complex is stable and to see how it fluctuate in the binding site. On Sat, Oct 5, 2019 at 8:33 PM Justin Lemkul wrote: > > > On 10/5/19 10:53 AM, Quin K wrote: > > Hi, > > > > *What should I pick for RMSD analysis of protein ligand complex? * > >

[gmx-users] RMSD analysis of protein-ligand complex

Hi, *What should I pick for RMSD analysis of protein ligand complex? * *What other analysis can be done for protein ligand complex? * Following are the options I have for least square fit and for RMSD calculation. MPPA is the ligand I used. Group 0 ( System) has 50085 elements Group

[gmx-users] [gmx-user] CGenFF 4.0 vs 4.1, complex MD simulation.

Hi, I'm using CGenFF 4.1 for a complex MD simulation however it seems parachem website is using 4.0 for parametrization. So I downloaded CGenFF 4.0 and and tried to get .ipt file and i got a python version error saying 4.0 is using an older version of python. 1. I was able to get .itp and .prm

[gmx-users] Panelty score for CGenFF

Hi I got some high penalty scores for CGenFF generated .str file for several atoms (Prepared for protein-ligand complex MD). Kindly let me know how to validate these value and change them if necessary. Molecules (.mol2) https://controlc.com/263a8d2c Penalty scores (.str)

Re: [gmx-users] RMSD analysis and stability

Thank you! What else should I be looking for? [image: mailcastr branding] Sent with Mailcastr <https://mailcastr.com/?utm_source=chrome-extension_medium=branded-email_campaign=BRANDING> On Sun, Sep 15, 2019 at 4:16 PM Justin Lemkul wrote: > > > On 9/15/19 5:30 AM, Quin K wrote:

[gmx-users] RMSD analysis and stability

Hi everyone! I have done a MD simulation for a protein structure at 310K (100ns) this is the RMSD at around 65 ns kindly comment on the stability. Will I have to rerun the MD? Kindly let me know how to decide stability by analyzing RMSD. For backbone

[gmx-users] MDrun Slow!

Hi When I do a mdrun it gives me a message saying, Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are

Re: [gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36

Thank you! On Wed, Aug 28, 2019 at 7:56 PM Justin Lemkul wrote: > > > On 8/28/19 10:21 AM, Quin K wrote: > > *Thank you!* > > > > *When I use following in add ion step for tutorial (ion.mdp) it gives a > > fatal error, however when I used cutoff instead of PME

Re: [gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36

w.charmm-gui.org/?doc=input/solution> > When you provide all the inputs and parameters, you can download the final > files (including all the *.mdp files) > I hope you find it useful. > > Best regards, > Reza > > > On Wed, Aug 28, 2019 at 1:22 PM Quin K wrote: >

[gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36

Hi Does anyone have *.mdp* files for Lysozyme in water (With CHARMM36 FF) tutorial given in following link. http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html I want to try this for a project I'm doing. There are 4 .mdp files ions.mdp

[gmx-users] [gmx-user] advantage of charmm force field over opls for protein md simulation and protein+Inhibitor md simulation

Hi, 1. Are there any advantages of charmm forcefield over opls-all atom ff, for protein md simulation and protein+Inhibitor md simulation? 2. Where can i find parameter files (.mdp files) for charmm 22 forcefield for gromacs? 3. Can CHARMM27 all-atom force field (CHARM22 plus CMAP for

[gmx-users] Should Cation Ligand be removed before MD simulaiton

Hi I'm hoping to use a protein for MD simulation and later for docking with Autodock vina. *However there is a Mg2+ cation ligand in the DPB crystal structure of protein. Should this be removed before MD simulation? *and replaced with lets say Na+ to keep the charge of protein zero. I'm hoping

Re: [gmx-users] Using windows to run gromacs

Abraham wrote: > Hi, > > There's some support for Windows and it works pretty well. Installation is > covered in the installation guide, but it can be a bit trickier than on > Linux. > > Mark > > On Sun., 20 Jan. 2019, 06:19 Quin K, wrote: > > > I hope

[gmx-users] Using windows to run gromacs

I hope to use windows 10 to run gromacs md simulation. Will i face any trouble with the results than using linux? Thanks in advance -- 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

[gmx-users] -1.8 Equilibration pressure during MD simulation

Hi I used lyzozyme in water tutorial by virginia tech for MD simulation of a protein, *pdb id = 2NT7*. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx -tutorials/lysozyme/index.html During equilibration step of MD simulation for a protein I got following results for pressure. Would

Re: [gmx-users] Protein preparation

Thank you. There are so many pdb structures for the protein I'm looking for. I'm not sure which one to pick. What should I look for when picking a protein pdb structure? I want to test for an inhibitor with the protein. Which of the following I should look for. Resolution Ligands Inhibitors

Re: [gmx-users] Protein preparation

if the structure of binding site(s) and important chain features remain the same ? For the 50 ns MD simulation I never fixed the protein. Regards Quin. On Sun, Mar 26, 2017 at 7:51 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/26/17 9:44 AM, Quin K wrote: > >> Hi >> &g

[gmx-users] Protein preparation

Hi I'm new to Gromacs. I have a question regarding protein preparation for MD simulation. I ran a 50 ns MD simulation but later found out that the protein has a charge. I found that there is a Mg2+ Ion in the protein crystal structure. Should I remove this Mg2+ ion from protein before addition