vas penu

I just resolved the issue, please change line around 102 : /PyContact/gui/VMDControlPanel.py def send_command(self, cmd): if self.tcpClientSocket: # Convert the string command to bytes before sending self.tcpClientSocket.send((cmd + "\n").encode('utf-8')) but...

use msm.pi[np.concatenate(msm.dtrajs_active)] instead.

Thanks for your reply. input file ****************************************************************************** # barostat on barostatpressure 1.01325 boxsize 117.9540023803711 148.80099487304688 127.14400482177734 coordinates structure.pdb cutoff 9 minimize 500 parameters parameters pme on restart on slowperiod 1...

HI, I attached screenshot, I see frame as DNA & RNA is not complex with protein. I can't be very sure it is wrapping issue. https://drive.google.com/file/d/1LmDsahUvFM2XYbgjNNdpxuDrhqbMWrfS/view?usp=share_link Regards Vas

attached : https://drive.google.com/file/d/1eA2Kt2AD0sU1hS3L0FvH65_7fybaNJnT/view?usp=share_link

Thank you.

Thanks for your reply. However, the code return with pdbs with empty coordinates (nan). mols = model.getStates() mol.write(f"molecule_{i}.pdb"). Output of pdb file : CRYST1 74.052 78.967 74.636 90.00 90.00 90.00...

I tried with given option, The kernel is interrupted after this error message. No output. Getting state Molecules: 0%| | 0/5 [00:00

FYI ... If I use single quote around O3' atom as follows .. atom1_alpha_Dihang_residue_6 = {'name': 'O3'', 'resid': 5, 'segid': 'RNAA', 'chain': ' '} it is causing syntax error ,...

The above issue is resolved in the Charmm force field. However, when I switched to amber forcefield for RNA. I am encountering the following issues. Looks like the default amber...