How to prepare .lib and .frcmod parameter files for ligands in AMBER forcefield?

More Yahyea Baktiar Laskar's questions See All

What will be the impact of ongoing wars and bombardments in global warming and pollution?

In the current wars in Ukraine vs Russia, and Gaza-palestine vs Israel , large-scale bombardments, missile attacks, grenades, firearms and ammunitions are used, leading to production of tremendous...

08 February 2024 5,529 0 View

How much loading dye should I add with the sample so that the protein sample will properly work in SDS PAGE?

I have prepared 12% of SDS gel and a sample concentration that needs to load 24 ul in each lane to fulfill the requirement of 4uM protein concentration and the maximum volume of the lane is 20 ul....

06 June 2023 4,734 1 View

How to solve the fatal error while using Gromacs?

I am using Gromacs MD simulation for protein-ligand complex using the following command after NVT Equilibration : gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx...

02 November 2022 6,754 2 View

What are the tools available for computational predication of chemical synthesis of a particular compound?

I'm trying to predict the retrosynthesis of an experimental compound from its SMILE string and 3D structure using IBM RXN Chemistry Server. I got some results but not sure about their reliability....

03 May 2022 7,445 3 View

What is applicability domain in QSAR studies?

What is the applicability domain in QSAR studies and how to estimate that? I tool (VLifeMDS) I'm using for QSAR model generation also provides applicability domain analysis. However, this giving...

07 June 2021 9,296 3 View

What HPLC Marker(s) should be used to detect anthocyanins in a sample?

What HPLC Marker(s) or standard is used to detect and quantify anthocyanins such as Delphinidin, Cyanidin in a given sample of plant extract?

23 February 2021 2,251 4 View

Can we consider a molecule as a "drug lead" if it has a positive charge in its structure?

Can we consider a positively charged molecule as a drug lead while designing a drug using computational tools?

07 September 2020 9,453 3 View

What is the best sensing technique for fever detection of COVID-19 and other viral fever patients?

Please propose best sensing technique for fever detection of COVID-19 and other viral fever patients

21 April 2020 2,980 2 View

Will anybody give his account or narration with respect to problems on application of sensors in industry?

19 November 2019 3,806 3 View

Do I need to take permission from the depositor to use chemical structures from pubchem?

I'm writing a chapter on medicinal plants and their merit in prevention and treatment of diseases. So I'm mentioning more than a dozen of phytocompounds and retrieving their structure form PubChem...

24 August 2019 9,094 3 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

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 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

Why don't d-orbitals split themselves, why does it take a ligand? why don't protons from ligand repel nucleus split d-orbitals?

why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...

03 August 2024 3,589 3 View

Why doesn't chromium 2+ ion use all its d-orbitals to receive lone pairs from six waters in [Cr(H20)6)]3+?

I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...

03 August 2024 1,370 1 View