VMD-L Mailing List

From: Sandip Mondal (sandchem13_at_gmail.com)
Date: Wed Apr 18 2018 - 13:18:42 CDT

Dear all,

  Thanks to all of you for your clarification.

Thanking you,
Sandip

On Wed, Apr 18, 2018 at 8:44 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> Hi Sandip,
>
> So if I understand correctly, you simply want to write a PDB for the frame
> 123 (or whatever), correct? You don't need a loo for that. Also, for
> writing pdb you don't need to open the file for writing the way you do for
> writing regular text files. Simply do this.
>
> set atoms [atomselect top "not water"]
> $atoms frame 123
> $atoms writepdb file.dpb
>
>
>
> Hope this helps,
> Chitrak.
>
> On Wed, Apr 18, 2018 at 10:29 AM, Sandip Mondal <sandchem13_at_gmail.com>
> wrote:
>
>> Dear user,
>>
>> I am new in writing tcl script. I wrote a simple script for writing
>> selected regions in pdb format from a dcd.
>>
>> The script is as follows
>>
>> set atoms [atomselect top "not water"]
>> set nf [molinfo top get numframes]
>> set out [open "file.pdb" w]
>> for {set i 0} {$i < $nf} {incr i} {
>> if {$i == 123} {
>> $atoms frame $i
>> $atoms writepdb $out
>> }
>> }
>>
>> Here 123th frame of a dcd is just for example. This script doesn't
>> write anything in that $out file, however it creates a new file which I
>> expect in $out file. Can you plz suggest the way.
>>
>> Thanking you,
>> Sandip
>>
>
>