VMD-L Mailing List

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Apr 12 2018 - 15:50:47 CDT

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
>>
>