[gmx-users] Water naming

[Erik Marklund]

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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