Percentage of potential SASA of ligands in Gromacs??

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 6,200 2 View

How to generate the wfn file in gaussian ?

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 7,311 0 View

How to guess time taken to complete a QM/MM job in gaussian ?

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 9,208 0 View

Suggestion for combing of processors on server??

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 2,608 0 View

Error in generation of frcmod of FES in AMBER ?

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 1,826 0 View

Query about FES cluster topology in GROMACS?

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 9,793 0 View

Occupancy of hydrogen bonding in VMD after molecular dynamics ?

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 2,652 0 View

Hydrogen bonding distribution in molecular dynamics simulation in gromacs?

08 September 2017 852 0 View

Error in MD by gromacs

06 July 2017 8,975 0 View

Consideration of one chain or two chains in MD by Gromacs

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 6,005 6 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Does Napabucasin soluble in dichloromethane and in ethanol?

I need to prepare a solution of Napabucasin (inhibitor of cancer cell stemness) in dichloromethane. The drug is expensive, so maybe somebody already tried to do it. If it is soluble, what is the...

02 March 2021 9,945 3 View

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 View

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

What is the state of the drug inside solid lipid nanoparticles (SLNs)?

I am a little confuse with the mechanism of solid lipid nanoparticles (SLNs). The main point of encapsulating drugs into SLNs is because some drugs have low solubility in water. Therefore, SLNs...

01 March 2021 3,703 3 View

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 View

Can Virtual Servers (remote dekstop manager) run heavy ANSYS Fluent CFD simulation ?

I have a virtual machine. My host Pc specs are not that good thats why i went for virtual servers. so basically my host pc has 8gb of ram with nvidia quadro k2200 4Gb DDR5 GPU ,processor intel...

01 March 2021 8,415 1 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

I'm a student and I have to produce a cell line with a knockin for the NRF2 gene with GFP. I have to put a promotor in front of the GFP because the gene will be too far away from the promotor of...

28 February 2021 7,127 2 View

Are protein samples in SDS compatible with ELISA?

I have used an AllPrep DNA/RNA/Protein Mini Kit QIAGEN kit to extract RNA and protein from my samples. At the end of the protein purification, I resuspend my protein in 5% SDS. Will these samples...

28 February 2021 7,370 3 View