Can someone recommend a MD force field for phosphorylated cysteine (3-oxoalanine)?

I would like to do classical MDS of a protein containing phosphorylated cysteine (3-oxoalanine) using GROMACS. Which force field should I use?

07 August 2019 7,344 4 View

Why Gromacs mmpbsa shows 'nan' in energy values?

I have performed simulation using gromacs. The protein is of two chains, I am trying to understand the changes in mmpbsa values between the two chains but I get following. What could be possible...

02 March 2019 1,935 3 View

Is it possible to create gromacs ndx file of two chains as a single index file?

I have performed a protein-protein simulation. I wish to see the change in binding between protein chain A & chain B. How to create a index files of chain A & B and do the analysis? Like GROUP 1 :...

02 March 2019 6,250 4 View

Can GROMACS perform molecular dynamics with different pH? If NO, what could be an easiest alternative?

I wish to study the change in interaction of the small molecule with the protein in respective to change in pH. GROMACS focuses most on protonation state and not directly on pH. So how can I...

01 February 2019 3,095 5 View

How to get the nano-particles of different shapes in 3D PDB?

We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get...

03 April 2018 3,981 0 View

Is it possible to draw the nano particles using software? If yes, what are they?

We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get...

02 March 2018 7,111 1 View

Could someone suggest a tool to find druglikeness of multiple compounds at a time (.sdf)?

05 June 2017 8,517 0 View

Why many of the drugs in market do not satisfy lipinski rule?

05 June 2017 2,142 5 View

What are the set of parameters and its normal value used in "Quantitative Estimate of Drug-likeness (QED)" predictions?

05 June 2017 7,745 0 View

When considering molecular dynamics simulation, which is more appropriate? A long run dynamics or multiple run dynamics?

03 April 2017 2,597 3 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Does the pressure(-600 mmHg) affects pH?

When I conducted the degassing experiment using decompression under anaerobic condition(and I used ferrous based chelating agent), the oxidized ferric were observerd. So, could you tell me the...

03 March 2021 4,892 5 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

Why am I not able to use all VEP programs for the in silico analysis of avpr1b SNP's?

Good day researchers I am busy analysing the predicted effects of certain SNP's in AVPR1b. When using the VEP prediction programs (SIFT, Polyphen, FATHMM, LRT, Provean, Mutation Assessor, and...

28 February 2021 5,197 1 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

Which database would give me this list of chemical components?

Dear colleagues: I would like to know if anyone knows of a database that gives me the parameters pH, K, K, Mg, P, C, N, Zn, Cu, Ni and Cd of common foods. I find a lot of information of proteins,...

26 February 2021 5,525 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

Why is NH4OH added in heavy metals limit test?

The limit test I'm referring to is USP method II. In this procedure you need to dropwise add 6N of NH4OH to the sample until it the pH is alkali. After that you need to dilute and add HOAc until...

23 February 2021 2,049 3 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View