Martin Juhás

5 Questions 7 Answers 0 Followers

Questions related from Martin Juhás

Recommend software for linking SMILES fragments with on attachment points?

Hi, can you recommend any software, or maybe it can be done easily also using common tools like rdkit, that can take SMILES containing attachment points (e.g. CCO[*]) and combine/link them...

12 July 2024 8,392 0 View

What are the reasonable Gaussian accelerated MD EGAMD_BOOST values?

Hi, I have recently experimented with GaMD in Amber18. When using only total potential energy boosting, the EGAMD_BOOST reached approx. 6. However, when I switched to dual boosting, the...

16 October 2022 4,478 0 View

How to use SMD to simulate binding of ligand?

Dear colleagues, I have some experience with MD for studies of drug-target interactions, mainly NAMD and Amber. For quite some time, I wanted to try studying the binding/unbinding process of the...

04 June 2021 8,618 3 View

RHF->UHF instability in chlorbenzene

Hi, I investigated the stability of the wavefunction of Cl-pyridine in Gaussian 16 at (HF/aug-cc-pvtz stable=opt), but the output stated there is RHF->UHF instability. I was under the...

01 January 1970 1,160 2 View

ChEMBL - Negative Percent Effect

Hi, I noticed very peculiar values in ChEMBL database related to type Percent Effect. I am talking e.g. about compound CHEMBL3450662, where the value of Percent Effect ranges (based on target)...

01 January 1970 6,488 5 View