Amber MD error? - FAQS.TIPS

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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 7,089 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 2,904 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 5,160 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 5,849 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 2,699 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 4,057 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 492 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 5,543 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 6,964 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 1,110 2 View

How do I replace a file with a more recent version of a paper that was uploaded to ResearchGate?

The paper in question is "Interpolation of Nitrogen Fertilizer Use in Canada from Fertilizer Use Surveys". This paper was very recently published by Agronomy (MDPI). Agronomy has, in the last day...

07 August 2024 9,934 3 View

How to solve g_mmpbsa error?

Program: g_mmpbsa, version 2024.1 Source file: extrn_apbs.cxx (line 152) Fatal error: Failed to execute command: $APBS pybYcUWA.in --output-file=pybYcUW.out

07 August 2024 6,066 0 View

How do you delete a duplicate pdf for the same paper on ResearchGate?

The first pdf file I uploaded had an error. So I uploaded an updated, corrected pdf of that paper with a different pdf name. I dpon't want the old copy to be download or read.

07 August 2024 9,508 1 View

AUX gas reading problem on QE with full MS and PRM method in one run?

Dear QE-users, In the method where full MS positive mode and PRM mode are used, we always get an incorrect auxiliary gas reading (41 instead of 25). This only happens in this method; other...

06 August 2024 4,953 0 View

JCPDS 65-7246 file please?

Dear Researchers Kindly share JCPDS 65-7246 file Thanks in advance

04 August 2024 5,613 1 View

Dirty and clean?

Hi everyone I need a file with a dirty and clean potato image

04 August 2024 7,199 4 View

How to change the version of the article full-text pdf file?

How to change the displayed full article text to its corrected version? In the file on the page of the journal where I published the article, there was an error in the text, the table is...

30 July 2024 3,229 2 View

Difficulty with permittivitt and Magnetic Permeability Calculations?

Difficulty with permittivitt and Magnetic Permeability Calculations Hello everyone, I have all the parameters related to the calculations of the permittivitty and magnetic permeability...

30 July 2024 5,206 1 View

How to do pca analysis of c-alpha atom of the protein?

i m interested in pca analysis of c-alpha atoms in gromacs for that i used the following gmx_mpi covar -s mdca.tpr -f mdca.xtc -o eigenvalca.xvg -v eigenvecca.trr -av average.pdb -n index.ndx but...

30 July 2024 1,607 1 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View