From: Sourav Ray (souravray90_at_gmail.com)
Date: Mon Feb 16 2015 - 00:41:26 CST

on another note, is it possible to convert .dcd. file into ASCII format?

On Mon, Feb 16, 2015 at 12:01 PM, Sourav Ray <souravray90_at_gmail.com> wrote:

> .psf file for defining the topology and .dcd file for the coordinates. it
> would be convenient to get all the frames in a single pdb file as
> processing will be much easier.
>
> regards
> Sourav
>
> On Mon, Feb 16, 2015 at 11:21 AM, Maxim Belkin <mbelkin_at_ks.uiuc.edu>
> wrote:
>
>> What do you have as input (file format and content)?
>>
>> On Feb 15, 2015, at 23:21, Sourav Ray <souravray90_at_gmail.com> wrote:
>>
>> I guess there is some misunderstanding, I would like all the frames in a
>> single .pdb file, that too sequentially (frame 1, frame 2...). Is it
>> possible somehow?
>>
>> On Fri, Feb 13, 2015 at 5:03 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu>
>> wrote:
>>
>>> set nf [molinfo top get numframes]
>>> set sel [atomselect top "protein"]
>>> for {set i 0} {$i < $nf} {incr i} {
>>> $sel frame $i
>>> $sel writepdb "protein-$i.pdb"
>>> }
>>> $sel delete
>>> mol delete top
>>>
>>> If there are multiple proteins use more specific selection text, e.g.
>>> use resids or something else.
>>>
>>> Maxim
>>>
>>> > On Feb 13, 2015, at 04:09, Sourav Ray <souravray90_at_gmail.com> wrote:
>>> >
>>> > Hello
>>> >
>>> > I have been trying to extract all the frames of a protein into a
>>> single PDB file. There is a code available currently in a thread here for
>>> extracting each frame in different PDB files:
>>> >
>>> > set nf [molinfo top get numframes]
>>> >
>>> > for { set i 0 } {$i < $nf } { incr i } {
>>> > set sel [atomselect top protein frame $i]
>>> > $sel writepdb $i.pdb
>>> > }
>>> >
>>> > Can someone please suggest a modification that works? Also, what if
>>> there are multiple proteins? Can we extract each one separately?
>>> >
>>> > Regards
>>> > Sourav
>>>
>>>
>>
>>
>