From: ROPÓN-PALACIOS G. (biodano.geo_at_gmail.com)
Date: Thu Sep 02 2021 - 09:48:15 CDT
When you generate psf and pdb after ion add you view all system ?
Enviado desde mi iPhone
> El 2 set. 2021, a la(s) 9:42 a. m., Krithika Unmesh <krithika17_at_students.cutn.ac.in> escribió:
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> 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.
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> I will write in detail various steps and trials I did.
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> 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.
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> Then, for solvation, I typed the following command in Tk Console:
> package require solvate
> solvate atp.psf atp.pdb -t 30 -o atp_wb
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> [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). ]
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> I, then, manually added Na+ ions, using Add ions from Modelling section of extensions.
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> 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 empty.
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