(no subject)

From: Krithika Unmesh (krithika17_at_students.cutn.ac.in)
Date: Thu Sep 02 2021 - 09:40:41 CDT

I was trying to simulate an ATP molecule using NAMD and VMD. I was
following various tutorials on NAMD available on internet. All the
tutorials are based on proteins. What I understood is, it is different from
ATP. While I was performing the minimization and NAMD run, it was running
without any error. But, the resulting dcd file is found to be empty. It
does not having any molecule. In fact I am not able to understand the
mistakes I am making.

I will write in detail various steps and trials I did.

I first loaded the pdb file in VMD. In fact, I collected three different
pdb structures. I then generated the psf file using Automatic psf Builder
from the extension menu in vmd. But, here also I was having doubts. ATP
contains 31 atoms without hydrogen and 47 with hydrogen. But, even before
generating psf files, the loaded molecule was found to contain 47 atoms and
to my surprise, after generating psf file, the number of atoms was reduced
to 43. I tried with all the 3 pdb files I collected and for all the three,
the same thing happened.

Then, for solvation, I typed the following command in Tk Console:
package require solvate
solvate atp.psf atp.pdb -t 30 -o atp_wb

[And I could not get how we could provide solvent models such as tip3p,
spce etc. But, here I could not find it in any step. Also, is it possible
to set a desired number of water molecules(of our choice, say 800 molecules
in a box with dimension 30A x 30A x 30A box). ]

I, then, manually added Na+ ions, using Add ions from Modelling section of

I then calculated the minimum and maximum value of x, y, and z coordinates
of to find the center and the length of each coordinate of the water box,
using libre calc.
In namd graphical interface, I set the time step to 1fs. So, for
minimisations, I gave 10^6 steps (0.1ns) and for dynamics 2*10^7 steps
(2ns). I selected NPT ensemble (with desired temperature and pressure), and
gave periodic boundary conditions (for which xsc file was generated using
the calculations from libre calc); also provided particle Mesh Ewald for
electrostatic interactions. In simulation space partitioning, I gave the
cut off distance as 12 A. All other simulation parameters, I used the
default itself. And gave NAMD Run.But then, the dcd file is found to be

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