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

From: FyD <>
Date: Thu, 16 Jan 2014 09:23:31 +0100

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 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

   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: where advantages
of the BD approach is described.

At the origin of this work is the paper of Cieplak et al for biopolymers:
See also the R.E.D. 'perl' paper:

You could look at the works of S. Abel in R.E.DD.B.

-- 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

Project name Linear n-alkyl phosphocholine detergents
Project code F-92

Obviously you could imagine more complex (linear or branched) cases for you:

Finally concerning sugar Glc units; you might be interested by the
work of Cezard et al.:

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:
>> [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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Received on Thu Jan 16 2014 - 00:30:03 PST
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