[gmx-users] Water naming

[Kavyashree M]

Sir,

I realise it may be due to the pbc. Its difficult to
bring it near Mg with any of -pbc mol/centre
etc.. calculations are fine but visualisation is
difficult.

Regards
Kavya


On Sun, Feb 16, 2014 at 12:29 PM, Kavyashree M <hmkvsri at gmail.com> wrote:

> Sir,
>
> I tried extracting water using trjconv with the ndx file generated
> using g_hbond. The water I was looking for was within 2Ang from
> Magnesium atom, according to g_hbond -contact. but whatever
> trjconv extracted was 122..Ang away.
>
> there were 2 chains, in 1 case correct water was extracted but in
> other case it was very far from Mg.
>
> Any suggestions are welcome.
>
> Regards
> Kavya
>
>
> On Thu, Feb 13, 2014 at 9:14 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
>
>> Dear Sir,
>>
>> Yes I can try with trjconv..!!  Thank you for the suggestion!
>>
>> Regards
>> Kavya
>>
>>
>> On Thu, Feb 13, 2014 at 4:55 PM, Erik Marklund <
>> erik.marklund at chem.ox.ac.uk> wrote:
>>
>>> Hi,
>>>
>>> I see. Can't trjconv extract the waters for you?
>>>
>>> Kind regards,
>>> Erik
>>>
>>>
>>> On 13 Feb 2014, at 11:10, Kavyashree M <hmkvsri at gmail.com> wrote:
>>>
>>> > Dear Sir,
>>> >
>>> > For extracting specific waters involved in Hbond from the pdb I am
>>> using
>>> > a small script wherein i have to use the only information given in the
>>> index
>>> > file, generated from g_hbond, that is the atom number. so I am not
>>> clear
>>> > with it even now. Also the same problem is there with the residue
>>> numbering
>>> > of SOL in the, maximum is 9999 and the it restarts with 0.
>>> >
>>> > I still did not get your suggestion sir, please excuse my ignorance.
>>> >
>>> > Regards
>>> > kavya
>>> >
>>> >
>>> > On Thu, Feb 13, 2014 at 3:33 PM, Erik Marklund
>>> > <erik.marklund at chem.ox.ac.uk>wrote:
>>> >
>>> >> Hi Kavya,
>>> >>
>>> >> Most (all?) gromacs tools ignore the atom indices in the PDB file
>>> anyway,
>>> >> so what you intend to do is straightforward.
>>> >>
>>> >> Kind regards,
>>> >> Erik
>>> >>
>>> >> On 13 Feb 2014, at 06:30, Kavyashree M <hmkvsri at gmail.com> wrote:
>>> >>
>>> >>> Dear users,
>>> >>>
>>> >>> I was analysing the hydrogen bonding interaction of proteins and
>>> water
>>> >>> in a simulation and was trying to extract specific water that forms
>>> hbond
>>> >>> using matrix and index files generated by g_hbond.
>>> >>>
>>> >>> But I found that the index file created using g_hbond has continuous
>>> >> water
>>> >>> labels byt the pdb file of the system from the same trajectory does
>>> not
>>> >>> have continuous labeling, eg, max atom number of water(SOL) is 99999
>>> and
>>> >>> then
>>> >>> it restarts from 0, similarly maximum residue label of water (SOL) is
>>> >> 9999,
>>> >>> then it restarts from 0.
>>> >>>
>>> >>> So if I want to use the number (of SOL) in index file generated from
>>> >> hbond
>>> >>> to extract respective atom in pdb file will be wrong. Kindly suggest
>>> me a
>>> >>> way out
>>> >>> of this.
>>> >>>
>>> >>> Thank you
>>> >>> Regards
>>> >>> Kavya
>>> >>> --
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>>
>>
>