I want to know that whether Kollman charges always positive or may be negative?
Whether a protein may have zero kollman charge?
Dear All, How to determine the SASA of different ligands in absolute values and percentage of their potential SASA in solution to estimate how buried they are in GROMACS. Thank you in advance.
03 April 2019 6,340 2 View
Hi all, I have gauss view (6.0.16) and gaussian16W for microsoft windows. I want to generate the wfn file. I have tried specifying of C:\path\molecule.wfn in molecular specification section...
11 December 2018 7,496 0 View
Hello everyone, I have run optimization of protein-ligand complex using QM/MM in gaussian. I did not find any criteria to find how much time will be taken to complete this job. Is there any...
10 November 2018 9,302 0 View
Hi everyone, We have HP server consist of 160 processors on 80 cores (i.e. each core has 2 processors). We want to utilize this server for molecular dynamics work. So we want to combine like 60...
02 March 2018 2,726 0 View
Hi everyone, I have to do Molecular Dynamics Simulations of a FE2S2 center containing protein. I need to generate the FE2S2.mol2 and FE2S2.frcmod files. I have used the antechamber and parmchk...
11 December 2017 1,949 0 View
Hi everyone, I have run the molecular dynamics of FES cluster containing protein in GROMACS. I got the error that FE and FES are not found in the amino acid database of force field. What can i...
10 November 2017 9,911 0 View
Hi everyone, I have done molecular dynamics simulation of protein with ligand in GROMACS. I am not much aware of occupancy of hydrogen bonds in complexes. What does occupancy of hydrogen bonds...
09 October 2017 2,775 0 View
Hi, I have run the MD of a protein by using Gromacs. I have generate the number of hydrogen bonds between protein and ligand by following command:- gmx hbond -f md_0_1.xtc -s md_0_1.tpr -num...
08 September 2017 981 0 View
Hi everyone, I have modellled a protein by phyre. I got the 5 residues in outlier, so I tried modloop to build loop. When I used this model in gromacs for MD by CHARMM37. I got this error:- Atom...
06 July 2017 9,076 0 View
Hi all, I have to do molecular dynamics of a protein. it is trimer of dimer. It has total 6 chains Although in dimer both chains have same amino acids. It has 6 ligands. Ligand interact via...
06 July 2017 6,125 6 View
I'm working on selecting antibodies against a recombinant protein that has a His-tag. My idea is to first bind the recombinant protein to a HisTRAP column and then use this column for an affinity...
07 August 2024 505 3 View
Is it the "elution buffer" or the "dialysis buffer"? Note: I'll be using NanoDrop OneC
01 August 2024 967 3 View
When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!
29 July 2024 488 0 View
My photocatalyst from solid waste red med. Dye is methylene blue My all parameter study is showing zero order. How to prove it further that the reaction in zero order?
29 July 2024 7,404 1 View
Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...
28 July 2024 2,136 4 View
I'm having problems with ion exchange chromatography. After applying my sample (a fluorescent protein), a preferential path inevitably forms. The matrix I use is DEAE-Sephacel. Could someone...
27 July 2024 6,605 0 View
I use 0.5% sarkosyl to solubilise recombinant proteins contained in Inclusion bodies of E. coli. sarkosyl very effeciently solubilizes proteins from Inclusion bodies and I am trying to use...
25 July 2024 5,001 2 View
I know the difference between instrumental LOD and method LOD but my query is - in case of any sample whose concentration is zero or not detected by the instrumental LOD, is it possible to get...
24 July 2024 6,592 5 View
"The Correlation between Nutrition and Transport Mechanism under Abiotic Stress in Plants: A Comprehensive Review" by Muhammad Saleem, Jianhua Zhang, Muhammad Qasim, Rashid Iqbal, and Li Song,...
23 July 2024 9,109 0 View
Currently I need to calculate detection probabilities (PD) from radar cross section (RCS) data. Beta distribution parameters for this RCS data are calculated and will be used in Swerling0...
22 July 2024 868 0 View