VMD-L Mailing List

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Fri Aug 01 2008 - 10:52:45 CDT

Hi Peter,

I have tried -compound chain / res / segment. All of them still give wired
bond connections. (It's a small peptide on the edge of the wrapped new unit
cell.) Is there anything that I can have done wrong? I have read the manual
carefully, but can't find any other hint to solve the problem. I dont know
whether I missed something. Thanks.

Jianhui

On 8/1/08, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> Hi Jianhui,
> try using the -compound option to enforce wrapping groups together (see the
> manual page for the possible options; generally -compound res works well if
> you're just worried about broken waters, -compound chain otherwise).
> Best,
> Peter
>
> Jianhui Tian wrote:
>
>> Hi,
>> I used pbctools to wrap my system for better visualization. The command
>> I used is {pbc wrap -center "resid 1" -all}. After all is finished, I see
>> broken molecules, which means the whole molecule is on the edge of the new
>> box, half of the molecule is on one side and half on the other side and
>> wired bond connecting them. How can I avoid such broken molecules?
>> Jianhui
>> Biocomputation
>> Rensselar Polytechnic Institute
>>
>