Good day.
I got a .cif file from a supplementary file in a paper, related to cellulose molecule which I want to use in my simulations. I run this code to change the format to pdb file for input of pdb2gmx code -----> babel -icif ncellulose.cif -opdb ncelluose.pdb
However after getting the pdbfile and running pdb2gmx -f ncellulose.pdb I get error : Error in user input: Invalid command-line options In command-line option -f File 'ncellulose.pdb' does not exist or is not accessible. The file could not be opened. Reason: No such file or directory (call to fopen() returned error code 2) I also checked the online Automated Topology Builder (ATB) and Repository and again the topology file cannot be built and it says that the file is invalid. Can somebody help on this issue I want to use this cellulose file for my simulations. Please find attached the .cif and converted pdb files. Thanks.
This problem is because you need to provide the forcefield parameters to gromacs, to this you first need to create the topol.top using any protein and then modify this file adding the force field of your interest and deleting protein information. The ligand force field (DRGGMX.itp) can be easily obtain from the PRODRG server (http://prodrg1.dyndns.org/submit.html), and need to be indicated into the topol.top (line ; Include forcefield parameters).
Good simulation
Let (X1, p1) and (X2, P2) be metric spaces and define metrics on X1 x X2 as follows: For x = (x1,22), y := (41,42) E X1 x X2, let (a) di(x,y) := pı (x1, y1) + P2(x2, y2), (b) dz(x, y) := V(21(x1, yı))2 + (P2(x2, y2))2. (i) Prove that di and d2 define identical topologies. (ii) Prove that (X1 x X2, dı) is complete if and only if Xi and X2 are complete. (iii) Prove that (X1 * X2, dı) is compact if and only if X, and X, are compact.
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