Maria Solis

6 Questions 5 Answers 0 Followers

Questions related from Maria Solis

FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE NN1?

I am working on an protein-ligand system. I made a psf file and pdb with topology and parameters files of this only directory toppar_c36_jul20, but when I ran min.conf file in Namd , it...

22 May 2021 2,174 3 View

How do I generate a psf file for ff-toolkit of vmd?

I was looking at using the vmd ff-toolkit to optimize that topology of a drug, but I see that it needs the psf of the ligand without hydrogens because the ff-toolkit program puts water on it. In...

18 May 2021 8,017 0 View

How can I create a psf file of a protein dimer in VMD?

I am using a script to create a psf file in VMD, then I hope use this psf file in namd. But the program generates a fault (photography). My system is a protein dimer: chain A (15-501), chain B...

15 April 2021 2,007 4 View

I have troubles to use Assemble2 to visualize RNA sructures

Hello guys! I have installed Assemble2 on "Windows", but when I opened the PDB file in Assemble2 to view the 3D structure, the software said that: "RNAVIEW is not able to annotate your 3D"....

01 January 1970 6,070 1 View

How restraint a ligand with a protein when the interaction is vand der Waals in gromacs?

Hello! I want to restraint my ligand with a protein in Gromacs. According the reference, specific atoms of the ligand are joined with the protein: R1 interacts with 459-462 amino acid...

01 January 1970 9,510 1 View

How could I add harmonic restraint to Magnesium in *.itp for Gromacs?

I generated files for minimization in Gromacs through Charmm-gui. But, when I was searching the bonds between Mg and amino acid in the section [bond], there were not. On the other hand, I could...

01 January 1970 5,172 5 View