VMD-L Mailing List

From: Aliasghar Alizadeh-Mojarad (ali.alizadehmoj_at_gmail.com)
Date: Thu Jul 28 2016 - 14:35:26 CDT

Dear Norman,
Yes, I already did it and I am trying to merge pdbs.

Best wishes,
Ali

On Thu, Jul 28, 2016 at 1:42 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> I guess not.
>
>
>
> With some TCL scripting you could write PDB files for each frames of both
> DCD file out of VMD, merge these PDBs and convert the PDBs to a DCD at the
> end.
>
>
>
> *Von:* Aliasghar Alizadeh-Mojarad [mailto:ali.alizadehmoj_at_gmail.com]
> *Gesendet:* Mittwoch, 27. Juli 2016 19:52
> *An:* Norman Geist <norman.geist_at_uni-greifswald.de>
> *Betreff:* Re: vmd-l: merging independent dcd files,
>
>
>
> Dear Norman,
>
> Thank you for your reply. I resolved that problem. But, my problem is
> another thing. I want to merge two different dcd files with two different
> number of dummy atoms. I made an index file including total number of dummy
> atoms.
>
> Does anybody know the developer of catdcd plugin? I even do not know it is
> possible to merge dcd files with different species and different number of
> particles or not.
>
>
>
> Best wishes,
>
> Ali
>
>
>
> On Wed, Jul 27, 2016 at 1:04 AM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
> If you run catdcd without argument it will print its usage information. It
> might be a good practice for you to figure this out by yourself, but:
>
>
>
> catdcd –o merged.dcd –otype dcd –dcd file1.dcd –dcd file2.dcd
>
>
>
> I think even shorter is possible with just:
>
>
>
> catdcd –o merged.dcd file1.dcd file2.dcd
>
>
>
> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Aliasghar Alizadeh-Mojarad
> *Gesendet:* Mittwoch, 27. Juli 2016 05:05
> *An:* Vmd l <vmd-l_at_ks.uiuc.edu>
> *Betreff:* vmd-l: merging independent dcd files,
>
>
>
>
>
> Dear VMD users,
>
> I have two independent dcd files containing dummy atoms and I want to
> merge them. In fact, they are parts of the same trajectory file. I
> extracted them to do some processing(translating species to new
> coordination). Now, I want to combine them into a new trajectory.
>
> I used catdcd plugin(I already searched in vmd mailing list) but I have
> problem with running catdcd. I got this error:
>
>
>
> >>catdcd
>
> wrong # args: should be "catdcdList dcdFileNames outFile indexFile stride"
>
>
>
> It means that I have no catdcd pluging? I downloaded the binary catdcd but
> I do not know how I can use binaries to add as vmd plugin.
>
> Is there another way to do it without using catdcd?
>
> I will appreciate any helps.
>
>
>
> --
>
> Sincerely,
> Aliasghar Alizadeh-Mojarad
>
>
>
>
>
> --
>
> Sincerely,
> Aliasghar Alizadeh-Mojarad
>
> 

-- 
Sincerely,
Aliasghar Alizadeh-Mojarad