Zeeshan Zafar

7 Questions 7 Answers 0 Followers

Questions related from Zeeshan Zafar

How to generat .itp, .gro and .prm file from Automated Topology Builder for GROMOS96 54a7?

I need .gro, .itp, and .prm file for heteroatom for simulations of TM-proteins. Automated Topology Builder is not generating these files. Similar is the case with PRODRG? Any suggestions please.

23 April 2022 941 4 View

Is there any alternative of MGAlignit, a tool for the alignment of mRNA with genomic sequences?

I want to align mRNA with the genomic sequence. I was using MGAlignit earlier but the server is not responding now. Do you know of any alternate tool?

27 March 2022 8,270 2 View

How much area per lipid is suitable during position restraining in GROMAC simulation of GPC?

Hi. I am running transmembrane protein simulation. I am confused at position restraining. During the shrinking steps using inflategro.pl script, tutorial mentions experimental value 0.69A but i do...

19 August 2021 5,879 5 View

Why can I not find all of my residues in model predicted by Swiss-Model?

I am trying to perform homology modeling using the swiss-model but I have found that the swiss-model gives the same number of residues as that of the template. Whereas my sequence has more...

22 January 2021 5,712 3 View

Can I predict properties of chemicals via any Bioinformatics tool?

I want to know chemical properties such as repellent tendency.

06 January 2021 4,920 3 View

Is there any alternative of LigPrep?

I was going to use LigPrep for ligand optimization but LigPrep is not opensource and I don't have a budget to buy. Please suggest to me any other Ligand Preparation Tool.

02 December 2020 723 4 View

Can I use Tween 20 instead of Tween 80 for Spore Suspension?

For Fungal Spore suspension, can I use Tween 20 instead of Tween 80 as both are detergents?

20 November 2020 9,460 2 View