Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Hi, I've recently used OPLS-AA for a similar calculation. It has the advantage that many atom types are already defined in Gromacs and that QM-based calculations give you reasonable charges. Note that it may take considerable simulation time (tens of ns) to discriminate between similar docke

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Lucio Ricardo Montero Valenzuela wrote: So it 's better to switch to the OPLS forcefield if I want to compute the charges?. How can I implement the OPLS-UA if my gromacs (version 3.3) only includes the OPLS-AA? We don't support United atom OPLS because Jorgensen himself does not use it anymore

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

So it 's better to switch to the OPLS forcefield if I want to compute the charges?. How can I implement the OPLS-UA if my gromacs (version 3.3) only includes the OPLS-AA? Mensaje citado por "Justin A. Lemkul" : > > > Lucio Montero wrote: > > How about MOPAC to calculate the charges for 3-methylade

[gmx-users] How to calculate the dihedral angle variations ???

Hi Everyone ! How can i see the variations in the "Cβ-S-S-Cβ" (Disulfide bridge) dihedral angle during a simulation ? Thanks in advance Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD ___ gmx-users mailing li

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

I have done the docking with autodock, and I want to do a MD satrting from the docked position. Mensaje citado por "Justin A. Lemkul" : > > > Lucio Montero wrote: > > How can you test the "ligands" when you don't know if they REALLY bind > > to the protein? > > > > Sounds like a job for docking an

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. Thanks for your information. Thanking you, Pawan On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul wrote: > > > Pawan Kumar wrote: > >> Respected Sir, >> >> Greetings from Pawan. >> Thanks for all your kind help and suggestions. >> I will work on this and

Re: [gmx-users] Energy Conservation with 4fs timestep

Joe Joe wrote: Hi, I get good conservation when running NVE in gromacs with 4 fs when I use PME-switch for electrostatics but not so good when I use switch. Any thoughts why that would be? Params shown below. Finite cutoffs (such as used with "switch") are intrinsically unlikely to conserve

[gmx-users] Energy Conservation with 4fs timestep

Hi, I get good conservation when running NVE in gromacs with 4 fs when I use PME-switch for electrostatics but not so good when I use switch. Any thoughts why that would be? Params shown below. Thanks, Ilya ; ; File 'mdout.mdp' was generated ; By user: ichorny (502) ; On host:

Re: [gmx-users] Elastic Network Model

On Mon, Mar 30, 2009 at 3:23 PM, Joshua Adelman wrote: > I am interested in potentially using gromacs to do some calculations on an > C-alpha based elastic network model of the protein that I'm working on. I'm > curious if other users have done similar types of calculations, and if so, > what prot

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Lucio Montero wrote: How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. That may not be a bad place to start, but any parameters applied to a Gromos molecule have to reproduce condensed phase thermodynamic observa

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Lucio Montero wrote: How can you test the "ligands" when you don't know if they REALLY bind to the protein? Sounds like a job for docking and/or binding energy calculations. -Justin -- From: "Ran Friedman, Biochemisches Inst." Sent: Friday

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

How can you test the "ligands" when you don't know if they REALLY bind to the protein? -- From: "Ran Friedman, Biochemisches Inst." Sent: Friday, March 27, 2009 2:35 PM To: ; "Discussion list for GROMACS users" Subject: Re: [gmx-users] HF/6-31G

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. -- From: "Ran Friedman, Biochemisches Inst." Sent: Friday, March 27, 2009 2:35 PM To: ; "Discussion list for GROMACS us

Re: [gmx-users] new block lactitol

ceste...@unsl.edu.ar wrote: Hi Justin Thanks for your answer. I had check the relevant sugar, but I still have the problem of parameterization of the open GLC ring that forms the lactitol molecule. Hence why parameterization is difficult :) But I maintain that all of the relevant functional

Re: [gmx-users] new block lactitol

Hi Justin Thanks for your answer. I had check the relevant sugar, but I still have the problem of parameterization of the open GLC ring that forms the lactitol molecule. If you know of a similar example please let me know. Thanks very much Carmen > > ceste...@unsl.edu.ar wrote: >> Hi All >> I am tr

[gmx-users] Does andersen thermostat work?

Dear users, I would like to know if andersen thermostat is fully functional in the current version of GROMACS, since I've found no available documentation. Thanks for your help, Camilo ___ gmx-users mailing listgmx-users@gromacs.org http://www.grom

[gmx-users] Lipid models for GROMOS96 53a6

Dear all, Please find topologies (.itp files) for the lipids DPPC, DMPC, POPC and POPG for the GROMOS96 53a6 force field in the User Contributions-Downloads-Topologies-Molecule Topologies section When using these files please cite: Kukol, A., 2009. Lipid models for united-atom molecular dynami

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. Thanks for all your kind help and suggestions. I will work on this and ask you if I have further doubts. Is it fine if I use the perl code given in wiki.gromacs.org/membrane-simulations for

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Marc Sir, Thanks for your information. Thanking you, Pawan On Tue, Mar 31, 2009 at 5:31 PM, Marc F. Lensink wrote: > On Tue, Mar 31, 2009 at 07:23:57AM -0400, Justin A. Lemkul wrote: > > > > Force fields have to be internally self-consistent, so using the > parameters > > from OPLS wi

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. Thanks for all your kind help and suggestions. I will work on this and ask you if I have further doubts. Is it fine if I use the perl code given in wiki.gromacs.org/membrane-simulations for solvation after the genbox step to remove extra waters from the hydroph

Re: [gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

On Tue, Mar 31, 2009 at 07:23:57AM -0400, Justin A. Lemkul wrote: > > Force fields have to be internally self-consistent, so using the parameters > from OPLS with Berger lipids will give spurious results. The only proper > combinations are Gromos/Berger or OPLS/converted Berger. as long as one

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. Thanks for all your suggestions. Is it possible to use the lipid.itp file from Tieleman sir's website in combination with GROMOS 96 force field without any modification ? If you want to use lipid.itp without any modification, you are r

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. Thanks for all your suggestions. Is it possible to use the lipid.itp file from Tieleman sir's website in combination with GROMOS 96 force field without any modification ? Is it fine if I use the Gromos/Berger force field combination for the system I am using ?

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. I have edited the lipid.itp file to add just one line extra " H atom from the opls_force_filed.itp " at the end of lipid interactions data and that works fine. I have done this after seeing the archives. It was given either I should ch

[gmx-users] Doubt regarding membrane protein in POPC bilayer

Respected Sir, Greetings from Pawan. I have edited the lipid.itp file to add just one line extra " H atom from the opls_force_filed.itp " at the end of lipid interactions data and that works fine. I have done this after seeing the archives. It was given either I should change the file for sigma an

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Justin A. Lemkul wrote: Pawan Kumar wrote: Respected Sir, Greetings from Pawan. I have used force constants of 10 in position restraint .itp files for proteins as suggested in Dr. Tieleman' s webisite for Inflategro. The mdp files are : The .mdp files look reasonable enough, althoug

[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Respected Sir, Greetings from Pawan. I have used force constants of 10 in position restraint .itp files for proteins as suggested in Dr. Tieleman' s webisite for Inflategro. The mdp files are : The .mdp files look reasonable enough, although I don't know why you are

[gmx-users] Announcing NMR validation web interface iCing

Hi there, We are happy to announce the iCing web interface to CING (http://nmr.cmbi.ru.nl/cing) that can validate your NMR data & structures online, running tools such as What If, Procheck, Wattos, ShiftX, etc.. Please direct your browser to: https://nmr.cmbi.ru.nl/icing You can send in your dat

Re: [gmx-users] how to define the dummy atoms in gromacs

He, Yang wrote: > Hi all users, > > I need to add some dummy atoms in my case. I know that I need to include the > section [virtual_sites] in the top file but I am not sure how to define them > in the itp file .Do I need to list these atoms in the section[atoms] ? Can > anyone of you give me so