VMD-L Mailing List

From: Sourav Ray (souravray90_at_gmail.com)
Date: Mon Feb 16 2015 - 00:31:42 CST

.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
>>
>>
>
>