[gmx-users] I: How to rolled up a polymer chain

Thu Sep 25 10:57:12 CEST 2014

Hi to all,
in order to find the position tangled of a polymer chain,

 i tried to follow the indication of hte page Polymer reported in the gromacs guide on line.
i created a file oplsaa.rtp and a file oplsaa.hdb as descrived there, and  i save the file on the folder oplsaa, also i created a file PE.pdb as reported in the same page, with the indication for create a chain of polyetilene of 6 monomers, and i saved this last file in the folder ....gromacs/src/

I start with the command pdb2gmx -f PE.pdb
i select the force field as 14 OPLS-AA/L
i select  none as water model (bacause it is a single polymer chain)

I got the message "residue ethB non found in the residue topology database, aminoacid.r2b"

I read that the software tried to open other files as aminoacids.rpt aminoacids.hdb and it doen't found the residue.

A that point i thought to modify the files aminoacids.rpt and aminoacids.rdb by write down what was in the files oplsaa.rtp and oplsaa.hdb in the files aminoacids.rtp and aminoacids.hdb.

Follow, I run the software with the comand pdb2gmx -f PE.pdb
wwith same force field and same none water.
i got the same message:"residue ethB non found in the residue topology database, aminoacid.r2b"

Questions are:
how i can do for load that residue?
What do you suggest to do for induce the software to load my residue?

Bests.

MARCELLO CAMMARATA
Ing., Ph.D.,

 3208790796

Il Mercoledì 24 Settembre 2014 3:45, Mohd Farid Ismail <mohd.farid.ismail at yandex.com> ha scritto:

I think you should take Dr. Lemkul's advice, that is to try with a small molecule system first.  In general, from what I've learned, you first need to create the .rtp file, and put it in the oplsaa.ff directory.  This is all assuming you want to use oplsaa forcefield.  Check out the .rtp file format in the manual, or look at the aminoacid.rtp file in the oplsaa.ff directory.  Then try pdb2gmx again.

But, I'm wondering whether what you're trying to achieve feasible?  IIRC I saw a review by Gary Grest and Kurt Kremer that for PE, it takes hundreds of nano seconds for 10 PE chains to equilibrate (for all atom model).  Who knows how long it would take for your system, polyamide.  Even with coarse-grain forcefield, it should take forever to equilibrate polymer melts.  Maybe this is a long time scale project (years before your get results)?  And if you want to use CG models, then there's no need to create detailed atomistic model with avogadro.  And there are other software that does this better, hoomd or lammps come to mind.

By no means I am trying to discourage you.  Someone has to try this.  The more people work on this, the more chances someone will come up with the answer.  I just wonder whether you actually have considered the issues with this kind of system and found a solution.

--Farid

24.09.2014, 02:16, "marcello cammarata" <mstaxmarcello at yahoo.it>:
yes, 
>
>i need yto know how it go to tangled, related with the lenght of chain, the number of chains in volume unit.
>For now the problem is that when i run pdd2gmx, i don't choose any solvent, because there isn't eny solvent, i choose only a kind of force field present in the database software. but each time it ask me for the LIG. 
>
>I have a bdp file with the chain, made by me.
> 
> 
>
>MARCELLO CAMMARATA
>Ing., Ph.D.,
>
> 
> 3208790796
> 
>
>
>
>Il Martedì 23 Settembre 2014 18:25, Mohd Farid Ismail <mohd.farid.ismail at yandex.com> ha scritto:
>
>
>
>Can I ask you something.  What do you mean by "rolled up"?  Do you mean create the tangled conformation of polymer chains?
>
>--Farid
>
>
>22.09.2014, 20:46, "marcello cammarata" <mstaxmarcello at yahoo.it>:
>> Hi,
>>  i had checked all the archives, i have read about 100posts in the last 2 month.
>> Nobody have problem similar to mine.
>> Problem for me are Two.
>> 1- instead i am a doctor, i am not able to find the right advice at your site.
>> 2- In your site there is no space for begginer user.
>>
>> The main pages where i checked are:
>> Residue
>> Chain
>> Polyethylene (PE) simulations in Gromacs - please!
>> .rtp File
>> Force Fields
>> Adding a Residue to a Force Field
>> Modifying a force field
>>
>> But i don't have find any suggestion for my problem.
>> Is there an other blog, that i can't see.
>> i have several of problem with Gromacs,
>> - in Cygwin it doen't work, i got a "bash" comand
>> - the topology need a lig parameters.
>>
>> one more time, below there is my post. I wpould like if you can help me to solve this question, instead i can try to use an othere MD software.
>>
>> MARCELLO CAMMARATA
>> Ing., Ph.D.,
>>
>>  3208790796
>>
>> Il Lunedì 22 Settembre 2014 14:20, marcello cammarata <mstaxmarcello at yahoo.it> ha scritto:
>>
>> My goal, for now, is to model a polimer (nylon-6) chain, and to find the equilibrium position of the chain considering the capacity to be rolled up itself.
>> I had create a pdb file using Avogadro software, but when i go to gromacs to input the
>>  data using the function pdb2gmx And indipendently of the force field that i
>>                           choose i get :that "Residue LIG not found".
>>
>> How to solve this?
>> thanks
>>
>> MARCELLO CAMMARATA
>> Ing., Ph.D.,
>>
>> 3208790796
>> --
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>
>--
>Mohd Farid Ismail
>mohd.farid.ismail at yandex.com
> 
>
>