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

Combining100 .gro files to just one .gro file?

Hello friends! I have 100 .gro files. How can I combine them and create just one .gro file? Thank you! Maryam

07 August 2017 8,750 1 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 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

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

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

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Why the results when using wall thickness and when using shell conduction are different in ansys fluent?

Actually, I am running cfd simulation for a heat exchanger which has two fluids one hot and other one is cold fluid. there is a solid domain between them, which I removed and instead I have used...

01 March 2021 9,537 2 View

Joint behaviour in Abaqus is not captured well?

I am working on roof joint and trying to simulate the behaviour in Abaqus. I am successful in running the model but the final graph does not follow the experimental curve in the negative direction...

01 March 2021 6,661 3 View