How to get .itp and .gro file from .pdb file for a ligand that has topology compatible to OPLS and CHARMM force field ?

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Is this a facetotecta nauplius?

This larva was captured using a plankton net in the Persian Gulf during the summer. I believe it may be a Facetotecta nauplius.

08 August 2024 3,746 4 View

Short Synthesis of Graphene Oxide from Natural Graphite Flakes?

I am in search of a modified Hummer's method, which can be used to synthesis graphene oxide within 6-8 hours. As I am a student it is not allowed for us to work after 5 in the laboratory. So I am...

01 August 2024 8,368 2 View

Some new emerging problems on application of RL for scheduling in IoT networks?

I have seen plenty of existing works on applied Reinforcement Learning (RL) policies for optimized scheduling in IoT networks including Q-learning, DQNs, and the newer ones including PPO for...

01 August 2024 8,754 2 View

Following click reaction in cell lysates, protein is immobile and remains at the top of the gel in SDS-PAGE?

I am using CuBr/THPTA for a click reaction in total cell lysates. I am facing issues with my protein sample in non-reducing SDS-PAGE where it's not migrating properly and most of it remains at the...

29 July 2024 950 4 View

Which filtration method to go for run off water from dirty solar panels to be used again?

We are working on a robot that cleans solar panels using fresh water supply and a rotating brush. We are trying to conserve as much water at possible by recycling the dirty water that is collected...

28 July 2024 5,778 2 View

How to make soil water characteristic curve using centrifuge?

We have no access of pressure plate apparatus

22 July 2024 3,488 2 View

When making abraxane with Nab tech, why is 9:1 Chloroform&EtOH used as solvents?

Is it the best optimization ratio based on experiments?

22 July 2024 8,170 0 View

Can diamond be grown using molecular beam epitaxy?

22 July 2024 9,755 2 View

What is the degassing temperature and time for biochar for BET surface area analysis if TGA is not possible?

Since BET and TGA both are very costly instruments and many places the facilities are not available (for large number of samples) hence a threshold degassing temperature and time is preferable

16 July 2024 8,112 2 View

Can we analyse RMSD for peptide-HLA docking and binding affinity for peptide-HLA to TCR docking, in a peptide-HLA-TCR docking ?

In the peptide-HLA-TCR docking process, can we express the result of peptide-HLA docking in RMSD and for peptide-HLA to TCR docking, can results be expressed in binding affinity?

11 July 2024 4,831 0 View

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

Do you think can be any gas and oil reservoirs in central of Iran?

I want to know more about gas and oil reservoirs in Iran.

14 July 2024 3,350 2 View

How to apply virtual site for a polymer?

Dear All, I have a PDB structure for a complex and large polymer. I need to perform MD simulations using the OPLS-AA force field. I obtained the force field parameters from LigParGen and created...

11 July 2024 5,109 0 View

Can I use different force field for protein and ligand?

Hello, Dear! Generally, I used CHARMM36 + cgenff force field for simulaiton. But,, due to certain parts of lignad, force field cannot be generated using Cgenff. Can I use different force field...

10 July 2024 9,513 3 View

Interested in Postdoc position in Mathematics at IMI-BAS BG?

Computational topology of solitons The well-established research area of algebraic topology currently goes interdisciplinary with computer science in many directions. The Topological Data Analysis...

08 July 2024 2,816 0 View

I found trouble to run MD of my peptide with PTM in different force field. In Charm-GUI, it cant recognize the engineering residue. What can I do now?

I am working on my PTM project. I have some peptide. I got the result of doing MD of those peptide without PTM in different force field like Charm-GUI, Amber, Gromacs. Now I have to do MD of those...

05 July 2024 9,346 0 View

How validate the dynamic molecualr simulation with experimental data?

I used forcite module of Material Studio software to simulate the dissolution of zinc production waste in deep eutectic solvent. UFF force field has been used for the optimization of molecules,...

02 July 2024 7,494 1 View

How to simulate a preprepared membrane model?

I have a membrane model files from a published work. I want to use that model for my research. Can anyone help me with how do I proceed with it. I have the PDB, PSF and STR files of the membrane....

28 June 2024 6,455 1 View

I tried to do simulation using YASARA software for an optimized ligand after docking but an error is coming what should I do?

The error message is "Angle parameter for atoms42-45-15 (cf-nu-ns) not found in the force field. Initialization is not possible, check atoms for incorrect bonds, then update the force field's...

27 June 2024 3,446 3 View

What is the actual distance covered during sit-to-stand test?

Fellows, We are analysing data from force platform to calculate the power based on the acquired force. However, the current formula consider the distance covered by the individual as the "height"...

26 June 2024 2,049 1 View