Re: [gmx-users] .pdb file for DNA

You can try also 3DNA: http://rutchem.rutgers.edu/~xiangjun/3DNA/ Regards Paulo A. Netz On Mon, Mar 7, 2011 at 3:40 AM, majid hasan wrote: > Dear All, > > I want to simulate interaction between single strand dna and cnt. I tried > to use Biomer (from case group webpage), but it's not work

Re: [gmx-users] DNA podophyllotoxin

DNA simulations are very sensitive to force field, topology and simulation protocols. In order to find out why this aggregation happened, some information is needed, such as how big was the DNA fragment, how were calculated the long-ranged electrostatic interactions... From your post I assume that

Re: [gmx-users] terminal phosphate residue for dna simulations

DA, DT, DC, DG). You just have to consider your terminal nucleotides as regular ones (i.e. named as DA instead of DA3 or DA5 and so on). More details you can find in my paper: doi: *10.1021*/*jp1035663* * * Best regards Paulo Netz On Tue, Feb 19, 2013 at 10:35 AM, Vedat Durmaz wrote: > hi g

Re: [gmx-users] terminal phosphate residue for dna simulations

xplicitly taken into account). Anyway, the corresponding modifications would be straightforward in GROMACS files. Best regards Paulo Netz On Thu, Feb 21, 2013 at 1:02 PM, Vedat Durmaz wrote: > > hi paulo & gmx, > > thank you for your time and hint! as far as i've un

Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond

No, this oscillation is related to libration. See, for instance http://www.princeton.edu/~fhs/rahman/rahman.pdf esp. Fig. 24 in this paper Best regards Paulo Netz On Tue, Apr 9, 2013 at 2:38 PM, Nilesh Dhumal wrote: > Is oscillation is because of change in hydrogen bonded distance? >

Re: [gmx-users] Intercalation DNA-Ethidium bromide

in the DNA structure, in order to sample the intercalation binding mode as a reasonable starting point for MD simulations. Best regards Paulo Netz On Thu, Sep 27, 2012 at 3:15 AM, Hovakim Grabski wrote: > Dear Gromacs users, > > I've been running several simulations involving 2

Re: [gmx-users] Restraining two Macromolecules

better solution is to write a short program (in C or FORTRAN) or script, which could filter out the numbering of non-hydrogen atoms. I hope it can help Best regards Paulo Netz Universidade Federal do Rio Grande do Sul Porto Alegre, Brazil On Wed, Oct 17, 2012 at 6:46 PM, Arman M. Soufiani wrote

[gmx-users] DNA-ligand simulation with AMBER FF

topology manually, but this became complicated for large ligands. What is the best way to construct ligand topologies with AMBER parameters, for using with GROMACS, provided that we DO NOT have the AMBER package? Thank you very much in advance. Paulo Netz

[gmx-users] DNA-ligand interactions with AMBER

topology manually, but this became complicated for large ligands. What is the best way to construct ligand topologies with AMBER parameters, for using with GROMACS, provided that we DO NOT have the AMBER package? Thank you very much in advance. Paulo Netz

Re: [gmx-users] Re: DNA-ligand interactions with AMBER

Thank you very much! Paulo Netz On 5/13/09, Alan wrote: > Please, take a look at acpypi.googlecode.com. I hope it can help you. > > Alan > > On Wed, May 13, 2009 at 06:12, wrote: > >> Subject: [gmx-users] DNA-ligand interactions with AMBER >> >> Dear Gro