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

From: FyD <>
Date: Fri, 17 Jan 2014 09:03:21 +0100

Dear Arun Kumar Somavarapu,

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

We got your email at 'contact_at_q4md...' and we are going to adapt
the server for you; Sometime today: 225 atoms will be the new limit
for R.E.D. Server Dev.

First see: vs

Yes, we can increase the max. number of atoms because the QM programs
interfaced by R.E.D. Server and R.E.D. Server Dev. can handle larger
numbers of atoms. That being said you will have to wait for the
geometry optimization step to be done; likely be time consummmming ;-)
Increasing this max. number of atoms is a never ending problem;
opening R.E.D. Server Dev. for 200 or 210 atoms; and what about 213
atoms as in your case?

Only if you use R.E.D. Server Dev./R.E.D. Python you will be able to
skip the time consuming geometry optimization step by setting OPT_Calc
= "Off1" in
We have internally discussed several times about adding this option in
R.E.D. Python; we have decided to implement it because it can be
useful is some cases but personally I do not like this option.


All that being said I would like to underline that I suggest you to
use R.E.D. Server Dev. _AND_ the building block approach. I do not
like this whole molecule approach as used by many people with
Antechamber, where the conformation of the big molecule is often not
controlled; obviously the same apply with R.E.D. Server and R.E.D.
Server Dev...

regards, Francois

> 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 the
> re (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
> _______________________________________________
> AMBER mailing list
> [9]
> --
> Arun Kumar Somavarapu
> Project Fellow,
> Dr. Pawan Gupta Lab,
> Protein Science and Engineering Dept,
> Institute of Microbial Tecnology,
> Sec 39-A, Chandigarh - 160036.
> Links:
> ------
> [1]
> [2]
> [3]
> [4]
> [5]
> [6]
> [7]
> [8]
> [9]
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Fri Jan 17 2014 - 00:30:02 PST
Custom Search