Regarding Molecular Dynamics Simulation?

More Anwesh Pandey's questions See All

GROMACS Protein Error?

I'm getting following error while pdb2gmx: Residue 2 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entry is not found in...

09 October 2019 6,929 2 View

Amber MD error?

I'm getting following error in Amber: > loadoff drug.lib Could not open file drug.lib: not found Could not open database: drug.lib Please help!!

06 July 2019 8,642 2 View

AMBER Antechamber Error?

I'm getting following error while executing following command: antechamber -i drug.pdb -fi pdb -o drug_bcc.prep -fo prepi -c bcc -s 2 Error: cannot run "/home/anwesh/softwares/amber14/bin/sqm -O...

06 July 2019 2,727 2 View

Analysis and Phylogenetic tree for a fasta file?

I have a *.fasta file through nanopore sequencing (Min Ion) of approx ~250MB. I'm having problem in its analysis via MEGA Software due to large file size. I need to select a particular bacterial...

05 June 2019 5,003 6 View

Molecular Dynamics Simulation of MetalContaining Ligands?

I'm currently working on metallic ligands (transition metals/complexes as ligands). For their MD Simulation, how to generate topology for ligand, kindly help?

04 May 2019 5,705 1 View

How to set up QM/MM calculations in Gaussian for Drug-DNA complex?

I have completed molecular dynamics simulation of some drug-DNA complexes, now I need to perform QM/MM calculations on the system. Please tell me as to how to set up a QM/MM calculation in...

09 October 2018 2,226 3 View

Regarding Data Mining Softwares?

Is there any software which could mine data from downloaded research articles (pdf format) as per one's requirement?

09 October 2018 3,897 5 View

Regarding MMPBSA Calculations?

Is there any methodology to increase the no of cores (for faster computations) being used in the command line for mmpbsa claculations: g_mmpbsa -f md_0_1.xtc -s md_0_1.tpr -n index.ndx -i...

06 July 2018 248 5 View

Regarding MD via AMBER?

I am performing MD simulation for drug-DNA complex using GROMACS via AMBER force field. At following step, the program shows an error: gmx genion -s ions.tpr -o solvated.pdb -p topol.top -pname NA...

04 May 2018 5,384 2 View

Regarding MD Simulation analysis?

Can someone let me know about what is and how to perform, Umbrella Sampling in Molecular Dynamics Simulations, performed via GROMACS?

04 May 2018 6,799 5 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Vikram Dalal

Hello Anwesh,

Probably you have not added all atom ligand in .gro file. You are missing 47 atoms in .gro file. Some times, if you do not mention the total atoms in .gro then also you got this error.

Just cross check it.

Batsaikhan Mijiddorj

Did you insert a ligand in the system using gmx? Probably, you should edit your topol.top before insert the ligand.

Otherwise, you should repeat the protocol carefully.

Best.