Robson Santos

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Questions related from Robson Santos

Sander Error on MMPBSA calculation: what may be causing this error?

[INFO ] Running calculations on normal system... [INFO ] Beginning GB calculations with /home/bio/anaconda3/envs/gmxMMPBSA/bin/sander [INFO ] calculating complex contribution......

02 January 2024 2,238 6 View

How to have GPU support for GROMACS with SYCL build for GROMACS using Intel Iris Xe Graphics GPU?

I would like to have GPU support for GROMACS, my GPU is Intel Iris Xe Graphics, so I was recommended to use SYCL support. So I would like to ask if anyone knows how to proceed to install...

18 December 2023 9,165 5 View

Does anyone know how to solve this CGENFF error?

I submited the lig_fix.mol2 file to genarate topology into a str file and got this messege error: "readmol2 warning: non-unique atoms were renamed. Now processing molecule LIG ... attype warning:...

18 July 2023 5,481 3 View

"Fatal error: Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values" How to solve this error?

I followed the gromacs tutorial precisely and in the equilibration step I am facing this error. I tried "tc-grps = System" but occurs the same error.

30 June 2023 9,022 3 View

"Import numpy as np ImportError: No module named 'numpy'" How to fix?

File "cgenff_charmm2gmx_py3_nx2.py", line 53, in import numpy as np ImportError: No module named 'numpy' I have python 3.5.2 version, NetworkX 2.3 and numpy-1.25.0 all pre installed but the...

28 June 2023 5,289 3 View

Ligand topology preparation using gromacs show de following erro, does anybody know how to fix?

After running this step to create ligand topology for molecular dynamic simulation protein-ligand complex: python3 cgenff_charmm2gmx_py3_nx2.py ligand ligand_fix.mol2 ligand.str...

26 June 2023 663 3 View

How do I fix issues in Make CGenFF topology for copper ion on charmm gui for molecular dynamic simulation?

I tried to generate charmm36 topology and parameter files for copper ions on laccase enzyme but it presents an error that says "No residue in CHARMM forcefield". So I've tried CSML Search to...

26 June 2023 5,279 1 View