VMD-L Mailing List

From: Jean-Patrick Francoia (jeanpatrick.francoia_at_gmail.com)
Date: Wed Apr 30 2014 - 13:18:42 CDT

Le 30/04/2014 15:05, Mayne, Christopher G a écrit :
> Jean-Patrick,
>
> As I mentioned before, SMILES only encodes molecular graph data, not
> coordinates. So to convert SMILES to PDB for more than a couple of
> residues you would have to solve the protein folding problem to start
> from connectivity data and arrive as a useful 3D structure. SMILES is
> really not the appropriate format for protein structures, in general.
>
> Perhaps if you told us what you are trying to do, we could be more
> helpful. Your original question was quite simple--are there tools to
> go from SMILES to 3D coordinates? Yes, there are, but they are
> designed for small molecules. You seem to be more interested in large
> protein structures.
>
> Regards,
> Christopher Mayne
>
>
>
>
>
>
>
> On Apr 30, 2014, at 1:37 AM, Jean-Patrick Francoia wrote:
>
>> Le 30/04/2014 08:23, Eduard Schreiner a écrit :
>>> there are examples coming with it. Still, I do not think it is a
>>> good idea to build a protein with 15000 amino acids with emc. You
>>> will get some amorphous mass.
>>>
>>> eddi
>>>
>>>
>>> On Tue, Apr 29, 2014 at 10:51 PM, Jean-Patrick Francoia
>>> <jeanpatrick.francoia_at_gmail.com
>>> <mailto:jeanpatrick.francoia_at_gmail.com>> wrote:
>>>
>>> Le 29/04/2014 21:11, Eduard Schreiner a écrit :
>>>> Hi all,
>>>>
>>>> I would also like to mention the free tool EMC
>>>>
>>>> http://montecarlo.sourceforge.net/emc/Welcome.html
>>>>
>>>> which I use a lot to build any type of amorphous system or
>>>> polymer without a specific secondary structure, all based on
>>>> SMILES definition of all the components.
>>>>
>>>>
>>>> eddi
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Apr 29, 2014 at 6:56 PM, Davide Provasi
>>>> <davide.provasi_at_gmail.com <mailto:davide.provasi_at_gmail.com>> wrote:
>>>>
>>>> Chemaxon has tools and Java libraries to convert smiles to
>>>> formats vmd can visualize
>>>> (e.g.
>>>> https://www.chemaxon.com/marvin/help/applications/molconvert.html)
>>>> It requires a license but it's free for non-commercial use.
>>>> the Corina web demo is also free and would generate high
>>>> quality 3D molecular structures.
>>>> http://www.molecular-networks.com/online_demos/corina_demo
>>>> these tools, however are optimized for small molecules;
>>>> I'm not sure how well they would perform on peptides, let
>>>> alone long proteins
>>>> good luck
>>>>
>>>> Davide
>>>>
>>>>
>>>>
>>>> On Tue, Apr 29, 2014 at 11:01 AM, Norman Geist
>>>> <norman.geist_at_uni-greifswald.de
>>>> <mailto:norman.geist_at_uni-greifswald.de>> wrote:
>>>>
>>>> I don't think this is possible even with scripting, as
>>>> "building" tools do
>>>> usually have a database with coordinate templates. How
>>>> could you otherwise
>>>> determine the position of the atoms while adding them?
>>>> VMD is more a
>>>> visualization-, than a building-tool, although it can
>>>> be used for
>>>> parameterization.
>>>>
>>>> Norman Geist.
>>>>
>>>> > -----Ursprüngliche Nachricht-----
>>>> > Von: owner-vmd-l_at_ks.uiuc.edu
>>>> <mailto:owner-vmd-l_at_ks.uiuc.edu>
>>>> [mailto:owner-vmd-l_at_ks.uiuc.edu
>>>> <mailto:owner-vmd-l_at_ks.uiuc.edu>] Im
>>>> > Auftrag von Jean-Patrick Francoia
>>>> > Gesendet: Dienstag, 29. April 2014 14:49
>>>> > An: vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>
>>>> > Betreff: vmd-l: Visualize a SMILES string
>>>> >
>>>>
>>>> > Hello,
>>>> >
>>>> > I wonder if there is a way to visualize a SMILES
>>>> string in VMD, and
>>>> > possibly in 3D. I did a bit of digging but found
>>>> nothing clear.
>>>> >
>>>> > How do you do that ?
>>>> >
>>>> > Regards
>>>> >
>>>> > JP
>>>>
>>>>
>>>> ---
>>>> Diese E-Mail ist frei von Viren und Malware, denn der
>>>> avast! Antivirus Schutz ist aktiv.
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>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Davide Provasi
>>>> Dept. of Structural and Chemical Biology
>>>> Mount Sinai School of Medicine
>>>> Icahn Medical Institute Building
>>>> 1425 Madison Avenue, Box 1677
>>>> New York, NY 10029-6574
>>>> Tel.:212-659-8618 <tel:212-659-8618>
>>>> Fax: 212-849-2456 <tel:212-849-2456>
>>>>
>>>>
>>>
>>>
>>> EMC seems to be exactly what I need. How many atoms do you have
>>> to handle by SMILES string ? It seems to be a lot, from what I
>>> saw on some websites.
>>>
>>> Would you have any usefull links to start ? The doc provided in
>>> the package is just documentation.
>>>
>>> Thanks
>>>
>>>
>>
>>
>> No, there is "only" 960 amino acids :) So, how would you translate a
>> SMILES chain that long into an exploitable PDB ?
>>
>> Regards
>

Ok, I will close the topic by bringing the solution I finally found, and
some explications as well, if somebody needs them in the future.

I'm trying to model a complex homopolymer of lysine. Some of you might
have heard about PAMAM or polyLysine, it's kind of the same thing (mine
are called DGL). Mine is a dendrigraft, so basically, the lysine are
polymerized either on their epsilon amine (pseudo peptidique bound), or
either on their alpha amine. It's a branched polymer, and there are
several generations of them: from 1, to 5. There are 8 amino acids for
the G1, and 960 amino acids for the G5. What we know about them is the
average number of epsilon bounds per DGL, and the average number of
alpha bounds. So each molecule of DGL is unique.

To model this kind of molecule, I first needed to generate them,
randomly. So, I wrote a python program to produce a SMILEs string
(strings are easy to use in programs) with the previousy mentionned
parameters. At the end, I obtain a HUGE string for a DGL G5, and
traditional programs like Avogadro just crash when they try to convert a
SMILEs string that long to 3D coordinates.

Because yes, I understand I need to have a file with 3D coordinates to
perform modelisation. What I needed was a program capable of generating
3D coordinates from a huge SMILES string.

I finally found what I needed: Discovery Studio Visualizer. The
visualization program only is free. With that, I have been able to
generate a PDB and a mol2file for all the generations, while I failed
with other programs for G > 3.

So, Thank you very much all of you for the help. Even if that wasn't
what I was looking for, I learnt some usefull stuff.

Regards

JP