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 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

Regarding Molecular Dynamics Simulation via AMBER Force Field?

I am carrying out molecular dynamics simulation of drug-dna system; after having had removed the nucleic acid from the complex when i proceed to to the MD via AMBER force field in UBUNTU system i...

02 March 2018 968 2 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

How to get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

How can the modification of garden soil cause global warming?

Hello, I am working on a soil project and I found a primary research article that tests how the modification of agricultural soil can cause global warming, using a thermal collector, however I...

02 March 2021 7,161 3 View

Does anyone know how to plot my station to a section plot on Ocean Data View (ODV)?

I made a vertical section plot with WOA .nc file on ODV, and now I want to plot my stations (csv. file) in it. Does anyone know how to import my points to the section? They are two different...

01 March 2021 3,610 1 View

Does anyone know to clarify these changes?

01 March 2021 1,290 2 View

How can I convert .vesta file to a .cif file?

I've used the "export data" option in Vesta software to convert my unit cell into a cif file however when I use that cif in atomsk it shows error such as "can't read the position of atom 0". If I...

28 February 2021 4,966 3 View

How can we use a hybrid element in Abaqus Dynamic/Explicit for impressible materials?

Hi, all! How can we use a hybrid element in Abaqus Dynamic/Explicit for impressible materials? I have not find the choice for explicit element in Abaqus CAE. I am wondering whether it is possible...

25 February 2021 9,936 2 View

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25 February 2021 5,713 1 View

Anyone that can help with Maxquant TMT16plex which is missing?

Hi I am very new to proteomics analysis. I have got raw files from core facility running thermofisher TMT 16plex 4 hours. I cannot find on maxquant the option TMT16Plex there is only up to 11...

25 February 2021 1,675 3 View

How to search for crystal structure for material with atomic position labelled?

I am using the crystallographic open database and materials project to search for cif file but the exact structure is not mentioned or how can I deduce that the given structure and atomic position...

23 February 2021 6,723 2 View