How can I calculate center of mass for a protein?

Hello every body I want to calculate the center of mas for a protein. I want to know which amino acid the center of mass hold on. pleas give me a full help. thanks

31 December 2017 328 8 View

How can you calculate salt bridges and hydrogen bonds for a specific part of the structure in throughout a trajectory?

Hello every body I want to calculate the pattern of salt bridges and hydrogen bonds between two specific part of the protein througut the for the 10 last ns of a gromacs simulation trajectory....

31 December 2017 217 3 View

Could i treat different stages of cancer cell line with the same drug?

Hi every body I work on Wnt/beta catenin signaling pathway. I have a drug which is effective on non metastatic SW480 cell line. I want to test it on metastatic cell line SW620. the pathway is...

11 December 2017 1,635 4 View

How can I calculate antrophy using gromacs?

Hello every body I want to calculate the antrophy amount of a protein-protein complex using gmmpbsa module of gromacs. I can calculate binding energy but not antrophy. If you have any...

11 December 2017 8,649 1 View

How should i define a calcium in pdb file?

hello I have a protein with a calcium ion. I edited the PDB file, renaming the calcium to CA, as atom name and atom type and pdb2gmx, runs successfully. but know I worry becuse some viewers...

01 February 2017 6,703 0 View

Could any one help me in peptide expression?

I want to express a 37 a.a, 43 a.a and 55 a.a peptides using pET His6 Sumo TEV expression vector with BioBrick polypromoter restriction sites (14-S). the vector host is XL1 blue and the company...

08 September 2016 5,212 3 View

How can I calculate the dihedral angle change of two helices using amber scripts?

I need to know the position of two helices in a structure in comparison to each other. so I should to calculate the variation of their dihedral angles versus time. there is an article in the...

05 June 2016 9,713 2 View

How could i get a free clash avarage structure from gromacs trajectory?

hello I have 200 ns simulation of a peptide and i want to calculate average structure of the simulation. I used this command: g_rmsf -f md.xtc -o rmsf.xvg -s md.tpr -ox av.pdb The resulting pdb...

05 June 2016 323 4 View

How can i designe a harker diagram for a tow atom crystal system?

I have a hard exam in x-ray crystallography. i need your help to pass it. i need a reference to understand phase problem solving. any help is appreciated.

04 May 2016 3,241 1 View

How could I refold Denileukin diftitox(ontak) after extraction?

Hi is there any instruction to refold Denileukin diftitox(ontak)? it is really vital for my project. every help is appreciate.

09 October 2015 4,923 0 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View