From: Nikolay Simakov (
Date: Fri Feb 27 2009 - 20:07:52 CST

Thank you John for reply,

I understand that VMD utilize simple distance method, still it should
work in my case.

I have install 1.8.7 with the same results. What is more interesting I
have try vmd 1.8.6 on windows machine and its give me perfect results. I
also have try different newline code and it still doesn't give me
anything positive.


John Stone wrote:
> Nick,
> VMD uses a simple distance-based bond search heuristic which can
> make mistakes in some cases. I'd suggest that you try using one of
> the new test versions of VMD 1.8.7 (rather than an older version) and
> let us know if you still have trouble. If you do, then you might see
> if running the autopsf plugin on your structure will assign correct
> bonds even when the model is in a single molecule.
> Cheers,
> John Stone
> On Fri, Feb 27, 2009 at 05:01:30PM -0500, Nikolay Simakov wrote:
>> Hi,
>> I have next problem. Then I load pdb file which has protein and lipids,
>> vmd create bonds between protein and lipids and do not create bonds
>> withing lipids. If I split protein and lipids into separate pdb files
>> and then load them separately everything is fine.
>> I am running vmd-1.8.6 under linux. I also try to downgrade and check is
>> it working or not and found that 1.7.1 is doing good.
>> Has anyone have similar problems?
>> Nick