Failure to run ANTECHAMBER for residues in UCSF Chimera

01 January 1970 1 7K Report

Dear all

I have a protein model (generated via homology modeling) for a long protein. When I tried to minimize the structure via UCSF Chimera (after adding hydrogen), I got an error message stating that "Failure running ANTECHAMBER for residue HIS".

(There are 51 histidine residues in this pdb file).

What are the cause and possible solutions for such error?

Thnx

Aashish Bhatt

Hi Jameel,

Please read about the amber Histidine naming list.

http://ambermd.org/Questions/HIS.html

I have not tried USCF chimera with antechamber but I think the problem is residue naming.

For the correct protonation state, you can use PDB2PQR and H++ servers.

Best Regards

Badges
Science topic

Similar topics
Phytochemistry
Extracts

More Jameel M. Abduljalil's questions See All

For a significant cooperation among different universities, let us start with selecting external examiners for PhD or MSc students?

For a significant cooperation among different universities, let us start with selecting external examiners for PhD or MSc students from other countries. Is it useful or not? It is possible or not ?

14 September 2020 6,444 3 View

What is the best drawing computer software (Graphics) in biological sciences?

I would like to draw a figure for nucleic acids strands in pipe-like appearance with some curvatures and colors. I want the figure to be attractive, not just a collection of dull thick lines.

26 April 2020 621 4 View

Are highly correlated factors from an exploratory factor analysis, due to an oblique rotation, good or bad?

If factors from an exploratory factor analysis are highly correlated with one another, does this indicate that the constituency items are measuring similar constructs? Or do the items measure...

26 March 2020 3,461 3 View

How are calculations of GSH and MDA concentrations in liver and kidney tissue of laboratory rats ??

Hi,,I need a method or equation for calculating the concentrations of Clutathione (GSH) and Malundaldehyde (MDA) in liver and kidney tissue of laboratory rats ...

16 February 2020 9,345 3 View

How we can control on the food spoliage by used plant extract??

Hi, im trying now to find away to used plant extract as anatural preservative instead of chemical preservatives.

10 February 2020 2,237 6 View

Thank you in advance..what is the simulation model that takes geometric design such as lane width into consideration and reflect that on behaviour?

Simulation model is actually affected by geometric design

29 December 2017 3,971 2 View

How to verify a good training set?

Many authors in the computer vision community use the entire training dataset to validate or test their methods... my question is what is the best metric/parameters that can be used to measure a...

25 December 2013 9,898 19 View

How can I add new page by php in moodle software?

I want to develop some pages in Moodle software, because I have a good idea to develop, but I don't have information how can I add a new page by php in moodle software?

30 November 2013 6,975 3 View

What is the relationship between architecture and the environment?

What is the relationship between architecture and the enviroment? How to let the design of building adapt with climate and the enviroment?

14 March 2012 7,611 1 View

Hi everyone for The 3rd ICCEET 2021

The 3rd ICCEET 2021 targets to bring together researchers, research scholars, and leading academic scientists to share and exchange their research results and experiences on civil and...

01 January 1970 2,187 1 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

What is the best way to keep an anaerobic chamber anoxic in the absence of hydrogen?

I'm a graduate student who works with an anaerobe, so I often work in an anaerobic chamber. I've been working on an assay that involves the steady-state of the quinone/ quinol pool. Anoxic...

03 March 2021 2,971 1 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

What techniques can I use to determine the miscibility of polymer blends?

The term miscibility refers to the single-phase state in thermodynamics. I do not mean the compatibility of different components. To determine the miscibility I know several techniques such as...

03 March 2021 4,107 4 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

Shall I skip the measurement model in SmartPLS?

Hello everyone, I had run a mediation model in SmartPLS using questionnaires that were already validated among my statistical population. A professor who edited my paper -though she is not...

01 March 2021 3,052 3 View

What is involved in morphological changes of SEM images of a substance?

In the sem analysis of CaCO3 nanaoparticles, the morphology images showed spherical shaped particles but the proposed morphology for these type of nanoparticles is trigonal. I prepared the...

01 March 2021 1,960 4 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

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

How to remove the residual PDMS on the silicon mold?

Incompletely cross-linked pdms are difficult to remove.

01 March 2021 798 3 View