Hello Everyone, I have a AUTODOCK docking PDB file for both Protein-Ligand-DNA Complex. I want to do simulation of these complex. but simulation failed due to unrecognized ATOM TYPES present into the DNA. So, can you please have any suggestions?
Hi,
I heard that, GROMACS software is good at running protein-ligand-DNA complex simulation. Provided that ligand is Ions..Cause I have seen, Ions (Mg+) being in simulations, hvaent seen bigger ligand molecules in simulations. But i guess it should work.
Have u tried using GROMACS for it ?
i did on GROMACS but the following error is raised when i utilized the AMBER99SB protein, nucleic AMBER94.
the error massage i attached in below.
The error message is quite informative. Check the structure: Make sure that all atom names in each nucleotide correspond to their equivalents in the force field file(s).
ok Kunal, i will follow up this.. but again the error raised from the ACPYPE server for ligand topologies generation.
I installed the ACPYPE according the https://code.google.com/archive/p/acpype/wikis/TutorialAcpype4Gromacs.wiki.
but when I run the acpype then the following error is arised:
==> Executing Antechamber...
==> * Antechamber OK *
==> * Parmchk OK *
==> Executing Tleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Tleap failed
==> ... trying Sleap
==> Executing Sleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `which: no sleap in (/usr/local/gromacs/bin:/home/arindam/Downloads/amber14/bin:/home/arindam/amber14/bin:/home/arindam/Downloads/amber14/bin:/home/arindam/amber14/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/home/arindam/.local/bin:/home/arindam/bin:/sbin:/usr/bin:/usr/sbin:/home/arindam/jackal_64bit/bin) -f sleap.in'
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'Ligand_AC.prmtop'
Total time of execution: 26m 59s
can you help for this solution?
Best regards
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