Gyration for a specific part of a protein?

Hey Guys, I have a ubiquitin, I am planning to claculate radius of gyration for residue 1 to 24 and 25 to 76. How can I make this? What command shall I use? Thank you. Maryam

11 December 2017 3,373 3 View

Warning message in gromacs for radius of gyration?

Hey Guys, I am calculationg radius of gyration for 1ubq. My reference file is a pdb file. and I cannot change it. So I have to deal with it!! The problem is that I receive 2 warnings: WARNING:...

11 December 2017 5,153 6 View

Unfolding in negative ion mode in gromacs?

Hi friends! I am running my simulations in negative ion mode, gromacs. The problem is that, my proteins completely unfold, and rotate badly. At the very begininng they start unfolding and...

10 November 2017 5,988 1 View

Unwanted rotation in gromacs?

09 October 2017 1,566 7 View

How to calculate radius of gyration using .gro files?

Hello! How can I calculate radius of gyration for the proteins using .gro files. We use .tpr and .xtc files to calculate R of G but right now I need to use my .gro files. Thank you.

07 August 2017 3,062 4 View

Buffer or additive for Mass spec in negative ion mode?

Hello friends, I am really really desparate right now! I am working in negative mode in Mass spec. I added formic acid+acetonitrile+water to my protein and I didn't receive any signal. I added...

02 March 2017 3,735 10 View

Paper or book about the relationship among salt bridge, protein, genetics and evolution?

Hello Friends, I look for a paper/book/website to study about the relationship among salt bridges / proteins/genetics and evolution. I have searched alot but I failed. Can you please advise me? Best,

01 February 2017 9,581 3 View

How to determine nterm only on central protein?

Hello everyone! I have 1 central protein in pymol with 6 surrounding proteins. I want to find a command to say: please select nterm only on central protein. How can I do this? Thank you.

01 February 2017 996 0 View

How to select only 1 atom in pymol?

Hi! How can I select only 1 atom in pymol? only 1 atom, instead of selecting residues. Thanks

01 February 2017 5,677 1 View

How to determine side chains which I have measured the distances between?

01 February 2017 9,159 9 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

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

Formulation of polymer color flakes

I am writing to request some information for making polymer color flakes. I would appreciate the help.

17 March 2021 0 0 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

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View