From: Tahmina Akter (takter_at_aggies.ncat.edu)
Date: Wed Jun 29 2016 - 12:07:10 CDT

PMMA is Polymethyle methacrylate. The PMMA structure I want is of 10
monomers and 72 chains. How can I generate the pdb?

On Wed, Jun 29, 2016 at 12:30 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> PMMA is? More details please.
> On Jun 30, 2016 03:49, "Tahmina Akter" <takter_at_aggies.ncat.edu> wrote:
>
>> Thank you all. I appreciate your comments. Can you please tell me how can
>> I build my own PMMA pdb?
>>
>> On Tue, Jun 28, 2016 at 4:10 PM, Pawel Kedzierski <
>> pawel.kedzierski_at_pwr.edu.pl> wrote:
>>
>>> W dniu 28.06.2016 o 20:50, Ashar Malik pisze:
>>>
>>> It is hard to make sense of the pdb you are using. What does it contain
>>> or supposed to contain? To make a PSF file you need to have a well formed
>>> pdb such that the atom types and residue names are defined in the topology
>>> file or vice versa.
>>> On Jun 29, 2016 06:32, "Tahmina Akter" <takter_at_aggies.ncat.edu> wrote:
>>>
>>>> Hello,
>>>> I am very new in VMD. I downloaded a PMMA pdb file from
>>>>
>>> Apart from what Ashar Malik wrote above: you use the standard CHARMM
>>> topology file which provide bonding, atom types and charges for
>>> biomolecular systems but not for arbitrary molecules. So not only the PDB
>>> file should be rewritten (to provide division into monomers, and unique
>>> atom names within monomers) but you also need a topology file for your
>>> system.
>>> There is a "Topology File tutorial" on
>>> www.ks.uiuc.edu/Training/Tutorials/ which you may find useful to
>>> understand the concepts and to create the topology file yourself in case
>>> you don't find something ready for PMMA.
>>> Pawel
>>>
>>> <http://www.wall.org/%7Elarry/onion3/pdb/>
>>>> http://www.wall.org/~larry/onion3/pdb/ .
>>>> Now I want to generate the psf file. I tried the AutoPSF. But it says
>>>> Error: failed on end of segment Molecule Destroyed By Fatal Error. I am
>>>> attaching what I did.
>>>>
>>>> Thanks
>>>>
>>>> Regards,
>>>>
>>>> Tahmina Akter
>>>>
>>>
>>>
>>