VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Thu Jan 04 2007 - 16:13:49 CST

No. I have an equilibrated membrane/water/ions system which I want to
combine with an equilibrated protein/water/ion system. I do not want to
lose all the water from both systems. So I want to make a hole to
accomodate the protein box. I know this may sound a little strange but I
think it is the best way for my system.
Regards
Cesar

nunolf_at_ci.uc.pt escribió:
> Hi Cesar
>
> Quoting Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>:
>
>> Dear all,
>> I would like to remove water molecules in a box. The number of water
>> molecules is huge and they are spread among several segments which
>> may also contain ions. Does anyone have an efficient tcl script for
>> doing this under vmd /psfgen ?
>> Thanks in advance
>> Cesar
>>
>>
>
> Supposing that your box has protein+water+ions.
> On the VMD console, if you type:
>
> set sel [atomselect top protein]
> $sel writepdb only_protein.pdb
>
> You will get a pdb file with only protein atoms.
> Is this what you want?
>
> Cheers,
> Nuno
>
>
>