Re: [AMBER] Antechamber Segmentation fault (core dumped)

From: Arun Kumar Somavarapu <>
Date: Thu, 16 Jan 2014 22:12:36 +0530


Thank you sir for nice explanation, I will try this method and get back
to you.

On 2014-01-16 13:53, FyD wrote:

> Dear Arun Kumar Somavarapu,
> I am going to repeat what S. Abel wrote in his last email: use R.E.D.
> Server or better R.E.D. Server Dev. at and in
> particular use the building block (BD) approach, which allows
> splitting a large molecule into elementary components...
> Let's take an example: a big molecule composed of two R1 & R2
> chemical groups:
> R1-R2
> R1-R2 can be obtained by using two BDs: BD1 and BD2
> R1-X + X'-R2
> X & X' are connecting groups, which are well chosen allowing
> splitting R1-R2 into two elementary components, i.e. two small
> _molecules_.
> Then during charge fitting charge constraints (again well chosen)
> are going to be used so that the X & X' groups are removed: two
> molecular fragments R1 & R2 are thus designed:
> R1-X + X'-R2 --> R1 + R2
> Finally the R1 & R2 parts can be associated to generate the
> input/large molecule:
> R1 + R2 --> R1-R2
> You will find examples of such a BD approach in R.E.DD.B.; see for instance:
> [1] where advantages
> of the BD approach is described.
> At the origin of this work is the paper of Cieplak et al for biopolymers:
> [2]
> See also the R.E.D. 'perl' paper:
> [3]
> You could look at the works of S. Abel in R.E.DD.B.
> [4]
> -- R.E.DD.B. code (if known)
> -- Molecule keyword
> -- Molecule name
> -- Author lastname x
> -- Theory level/Basis se
> Text: Abel
> Search... [Done]
> Result(s) for search by Author name Abel
> Project name Glycolipids
> Project code F-72
> [5]
> Project name Linear n-alkyl phosphocholine detergents
> Project code F-92
> [6]
> Obviously you could imagine more complex (linear or branched) cases for you:
> R1-R2-R3-R4-R3-R4
> Finally concerning sugar Glc units; you might be interested by the
> work of Cezard et al.:
> [7]I hope this helps,
> regards, Francois
> I am trying to run MD for a docked complex, the ligand is pretty big which contains a hydroxymethylconduritol unit and a 4-amino-4-deoxy-D-chinovose residue linked to number (8-12) of a-D-glucose units. i was able to run antechamber for some small molecules successfully, but i struck with this molecule. please give me a brief idea to break and build the molecule or otherwise how to incorporate glycam force field in to Amber or any other way to go about it. On 2014-01-15 22:15, David A Case wrote: On Wed, Jan 15, 2014, Arun Kumar Somavarapu wrote: In your earlier message you suggested me to break the molecule, as i am new to Amber may be i will generate files for individual piece but i have no idea about next steps (like how to link and proceed). Linking sugars together to form poly-saccharides is a bit of a specialized task. Go to the online glycoprotein builder: [8] [1] and see if that will do what you want. Detailed questions posted there (or
here) usually get answered pretty quickly. But you will have to give details about your chemistry: just saying that what you have is "similar to glucose" is not enough. If the web site above doesn't help (enough), post *exactly* what you tried and the what the problem was. ...dac

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Arun Kumar Somavarapu
Project Fellow,
Dr. Pawan Gupta Lab,
Protein Science and Engineering Dept,
Institute of Microbial Tecnology,
Sec 39-A, Chandigarh - 160036.
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Received on Thu Jan 16 2014 - 09:00:02 PST
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