VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Sun Mar 08 2015 - 12:33:29 CDT

I want to achieve the result I would get if I write this command while
looping around without writing line 2 as it is.

set residlist {1 2 3 4 5}
set sel [atomselect top "resid 1 2 3 4 5"]
$sel writepdb out.pdb
$sel delete

Regards,
Monik

On Sun, Mar 8, 2015 at 10:47 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
wrote:

> Thanks Joaquim. Actually i set N outside the loop. What i want is to write
> all the coordinates in a single pdb file. As an example, something like
>
> If my molecule is water,
>
> Resid atomname coordinates
> 1 H1 .........
> 1 H2 ........
> 1 OH .........
> 2 H1 .........
> 2 H1 ..........
> 2 OH .........
> .
> .
> .
>
> Regards,
> Monika
>
> Monika Madhavi
> Department of Physics
> University of Colombo
> On Mar 8, 2015 10:11 PM, "Joaquim Rui de Castro Rodrigues" <
> joaquim.rodrigues_at_ipleiria.pt> wrote:
>
>> Dear Monika,
>>
>> I don't quite get what you are trying to achieve... Do you want to get
>> separate PDB files for each resid?
>> Anyhow, I see a few problems with your script:
>> - the for loop contains a strange comparison: $i<N. I just tested this
>> and it results in an infinite loop. You must set N outside of the loop.
>> - you're looping over resid's, but always writing to same the same file
>> (out.pdb)
>> - you're building atomselections at each iterations without deleting
>> them. Your script should crash vmd at some point.
>>
>> The following script should write resid's to separate files:
>>
>> set N 10
>> for {set i 0} {$i<$N} {incr i} {
>> set sel [atomselect top "resid $i"]
>> $sel writepdb [format out.%05d.pdb $i]
>> $sel delete
>> }
>>
>> Hope this helps,
>> J Rui Rodrigues
>>
>>
>> ________________________________________
>> De: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] Em Nome De Monika
>> Madhavi [monikamadhavi_at_gmail.com]
>> Enviado: domingo, 8 de Março de 2015 14:33
>> Para: vmd-l_at_ks.uiuc.edu
>> Assunto: vmd-l: How to write coordinates to a pdb without replacing
>> existing entries
>>
>> Dear all,
>>
>> I want to write coordinates of some selected molecules to a separate pdb
>> and I want to add the entries to the same pdb file for each molecule I
>> select in each iteration of the for loop.
>>
>> I used this tcl command
>>
>> set outfile [open out.pdb w]
>> for {set i 0} {$i<N} {incr i} {
>> set sel [atomselect top "resid $i"]
>> $sel writepdb out.pdb
>> }
>>
>> this code keeps writing the coordinates of each selection to a new file
>> at each iteration so at the end I only have the coordinates of the last
>> atom selected. How can I keep writing the coordinates to the same pdb
>> without deleting the old entries. Any help is greatly appreciated.
>>
>> Regards,
>> Monika
>> --
>> W.A.Monika Madhavi
>> Lecturer (Probation),
>> Department of Physics,
>> University of Colombo.
>
> 

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.