Re: [gmx-users] DNA-Protein complex

> I think you don`t need to build topology separately. Using appropriate force field will do. For protein-DNA simulation amber99sb works well. Amber99bsc1.ff is a new module available for gromacs users. You may use them or it is always better to refer literature to use the more appropriate

Re: [gmx-users] DNA-Protein complex

Check the literature to see what others that are simulating similar molecules are using and looking to study similar "things" (energies, structures etc) that you are. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash

[gmx-users] DNA-Protein complex

I am new in the field of molecular dynamics and simulation. I am trying to learn online tutorial for gromacs. I have docked my DNA with protein in HADDOCK. I want to run a simulation in gromacs. Can I make topology file of the complex together or I need to make topology file separately. Which

Re: [gmx-users] DNA-protein complex distorted in vacuum simulation

On 25 Mar 2015, at 11:43, rahul dhakne rahuldhakn...@gmail.commailto:rahuldhakn...@gmail.com wrote: NOTE 1 [file topol.top, line 44]: System has non-zero total charge: -163.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic

[gmx-users] DNA-protein complex distorted in vacuum simulation

Dear all Gromacs user, I minimized the energy of my DNA-protein complex with steep, l-bfgs integrator, and then ran the mdrun with integrator = md in vacuum. Upto energy minimization part it ran fine. When I submitted the minimized structure for mdrun (vacuum), protein and DNA part jiggles

Re: [gmx-users] DNA-protein complex

The force field that I used was ambe99bsc0, and my input file was: ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for

Re: [gmx-users] DNA-protein complex

2015-03-18 5:26 GMT-03:00 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl: The force field that I used was ambe99bsc0, and my input file was: ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps]

Re: [gmx-users] DNA-protein complex

On 3/18/15 4:26 AM, Urszula Uciechowska wrote: The force field that I used was ambe99bsc0, and my input file was: What is the DNA sequence? We have seen some cases where AMBER99-parmbsc0 fails to capture global characteristics of DNA structure. This is a common problem among additive

[gmx-users] DNA-protein complex

Hi, I am running MD for dsDNA-protein complex. After 50ns I observed that the DNA is unwinding. What did go wrong? Should I have changed something in my input file? Thank you in advance for your suggestions. best regards Urszula - Ta wiadomość została

Re: [gmx-users] DNA-protein complex

2015-03-17 14:35 GMT-03:00 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl: Hi, I am running MD for dsDNA-protein complex. After 50ns I observed that the DNA is unwinding. What did go wrong? Should I have changed something in my input file? You might want to send your input

Re: [gmx-users] DNA-Protein complex MD failing

Hi, Thanks for your reply, I am using  AMBER99SB-ILDN protein, nucleic AMBER94...about the settings, of that I am not certain since I took the parameters for a couple of papers and an example .mdp I found googling but not with the exact Amber force field. Then I modified it to use gpu so

Re: [gmx-users] DNA-Protein complex MD failing

On 2/20/15 7:21 AM, virginia miguel wrote: Hi, Thanks for your reply, I am using AMBER99SB-ILDN protein, nucleic AMBER94...about the settings, of that I am not certain since I took the parameters for a couple of papers and an example .mdp I found googling but not with the exact Amber force

Re: [gmx-users] DNA-Protein complex MD failing

On 2/19/15 12:55 PM, virginia miguel wrote: Hi everyone; I am tryingto run a simulation of a DNA-protein complex obtained by docking of a dsDNA of18bp to a crystal structure of the recA protein using GPU. I used amber ff, adodecahedron cell with 15A of distance from the surface of the

[gmx-users] DNA-Protein complex MD failing

Hi everyone; I am tryingto run a simulation of a DNA-protein complex obtained by docking of a dsDNA of18bp to a crystal structure of the recA protein using GPU. I used amber ff, adodecahedron cell with 15A of distance from the surface of the complex and neutralizedwith counter ions (42 NA+,

Re: [gmx-users] DNA-protein complex - which force field to use?

Hi, On 02/02/15 10:18, Erik Marklund wrote: On 2 Feb 2015, at 01:53, Jernej Zidar jernej.zi...@gmail.commailto:jernej.zi...@gmail.com wrote: Hi everyone! I would like to study a DNA-protein complex. The protein part is composed of aminoacids covalently attached to the DNA bases. Which

Re: [gmx-users] DNA-protein complex - which force field to use?

Hi Jernej I'll choose AMBER or CHARMM, because these two forcefields have a more reliable description of nucleic acids. In my experience, OPLS-aa and GROMOS do not seem to be able to produce stable simulations in the large time scale for nucleic acids systems. Best regards Paulo Netz

[gmx-users] DNA-protein complex - which force field to use?

Hi everyone! I would like to study a DNA-protein complex. The protein part is composed of aminoacids covalently attached to the DNA bases. Which force field would you recommend? Based on recent experience I was thinking of using either OPLS-aa or CHARMM. OPLS-aa would be the prefered choice