VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Jun 29 2016 - 11:30:14 CDT

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
>>>
>>
>>
>