On 7/18/17 8:15 AM, S M Bargeen Turzo wrote:
Hey I have been trying to convert S100A8A9(has two chains) to .gro but
after energy minimization I am not getting an integer for the total charge
of the system.
What is the magnitude of this non-integer charge? Did you do anything funny
during
Hey I have been trying to convert S100A8A9(has two chains) to .gro but
after energy minimization I am not getting an integer for the total charge
of the system.
Secondly when I try to do molecular dynamics simulation using these
parameters:
; 0.5 ps NVT production with Langevin thermostat and
Thank you very much for your help Justin. I really appreciate
I would like to bother you for one last time ( as of now ;). So, if I
am dealing with a non-trivial molecule like CNT or some
polyelectrolyte and I mainly intend to demonstrate the non-bonding
interactions with some nucleic acids (say
On 5/31/15 8:37 AM, soumadwip ghosh wrote:
Thank you very much for your help Justin. I really appreciate
I would like to bother you for one last time ( as of now ;). So, if I
am dealing with a non-trivial molecule like CNT or some
polyelectrolyte and I mainly intend to demonstrate the
Hi all,
I have a general query about the basic functioning of pdb2gmx. I
recently observed that when I take a PDB file for a DNA molecule and build
its topology via pdb2gmx (in CHARMM27 ff) it automatically builds it
without any hitches. If I look at the .itp file made for the DNA chain it
On 5/30/15 6:40 AM, soumadwip ghosh wrote:
Hi all,
I have a general query about the basic functioning of pdb2gmx. I
recently observed that when I take a PDB file for a DNA molecule and build
its topology via pdb2gmx (in CHARMM27 ff) it automatically builds it
without any hitches. If I
Thanks Justin for your insights.
So when I am making the topology of DNA via ppdb2gmx using CHARMM, the
parameters in the .itp files are not adequate and I should place them
manually everytime I make a molecule topology with pdb2gmx? In some of
my previous works actually the DNA molecule gave
On 5/30/15 10:24 AM, soumadwip ghosh wrote:
Thanks Justin for your insights.
So when I am making the topology of DNA via ppdb2gmx using CHARMM, the
parameters in the .itp files are not adequate and I should place them
manually everytime I make a molecule topology with pdb2gmx? In some of
my
