VMD-L Mailing List

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Thu Apr 12 2018 - 18:44:28 CDT

Thanks to all of you for clarification and tips. The way prof. Simmerling
suggested is quite straightforward.
Stefano

2018-04-12 22:50 GMT+02:00 Carlos Simmerling <carlos.simmerling_at_gmail.com>:

> I usually create 2 representations for the water - one using the atoms O
> and H1 and another using atoms O and H2.
>
> On Thu, Apr 12, 2018 at 3:57 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> wrote:
>
>> +1 for using a different representation. VDW is awesome, and usually you
>> just don't show your waters. :)
>>
>> -Josh
>>
>>
>>
>> On 2018-04-12 12:14:31-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>>
>> This is a well-known artifact due to the fact that many simulation
>> packages (but not NAMD, oddly enough) flag rigid water molecules by putting
>> a bond between the hydrogen atoms inside the topology. I don't believe
>> there is any automated solution to the problem other than to: 1) infer
>> connectivity by some method other than the topology (e.g. a PDB) , 2)
>> manually remove the bond, or 3) use a different representation.
>>
>> HTH,
>> BKR
>>
>> On Thu, Apr 12, 2018 at 10:03 AM, Stefano Guglielmo <
>> stefano.guglielmo_at_unito.it> wrote:
>>>
>>> Dear vmd users,
>>> I'm not sure whether this is an issue for vmd list: but I generated a
>>> hydrated system with amber force field (AmberTools16), but when visualizing
>>> the system in VMD water molecules appear as triangles, as if there were
>>> also a bond between the two hydrogen atoms.
>>> Does anyone has an idea about the reason?
>>>
>>> Thanks
>>> Stefano
>>>
>>> --
>>> Stefano GUGLIELMO PhD
>>> Assistant Professor of Medicinal Chemistry
>>> Department of Drug Science and Technology
>>> Via P. Giuria 9
>>> 10125 Turin, ITALY
>>> ph. +39 (0)11 6707178
>>>
>>
> 

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178