Many thanks to all.
The working combination of command lines is:
trajin ../3_/sm_md3.mdcrd 1001 2000
trajin ../4_/sm_md4.mdcrd 1 2000
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il
________________________________________
From: Eiros Zamora, Juan <j.eiros-zamora14.imperial.ac.uk>
Sent: Thursday, September 10, 2015 1:37 PM
To: AMBER Mailing List
Subject: Re: [AMBER] cpptraj script for average 3D protein structure?
Hi Dr. Shokhen,
If I’m understading your problem correctly, you should do
> trajin ../3_/sm_md3.mdcrd 1001 2000
> trajin ../4_/sm_md4.mdcrd
And that should correspond to the last 30ns of your MD simulation.
It’s the complete md4 file (which has the 20ns after the md3 file) and you only load the last 10 ns of the md3 file, making up the desired last 30 ns. Frame 2000 of md3 and Frame 1 of md4 should be consecutive so that covers the border between the two directories.
Hope that works for you,
Juan
> El 10/9/2015, a las 11:11, Michael Shokhen <michael.shokhen.biu.ac.il> escribió:
>
> Hi Matej,
>
> Thank you for relay.
> Unfortunately, your variant
>
> trajin ../4_/sm_md4.mdcrd 2000 4000
>
> selects snapshots inside the 4_ directory.
> In contrast, the problem is how to select
> snapshot from the time interval that covers the
> border between two directories 3_ and 4_ as I wrote
> in my example.
> The question is still open.
>
> Michael
>
>
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il
>
> ________________________________________
> From: Repic Matej <matej.repic.epfl.ch>
> Sent: Thursday, September 10, 2015 12:58 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] cpptraj script for average 3D protein structure?
>
> I think adding another line after the trajin 3_ would do the trick:
>
> trajin ../4_/sm_md4.mdcrd 2000 4000
>
>
> Best,
> Matej
>
> ------------------------------------------------------
> Dr. Matej Repic
> Ecole Polytechnique Fédérale de Lausanne
> Laboratory of Computational Chemistry and Biochemistry
> SB - ISIC LCBC
> BCH 4108
> CH - 1015 Lausanne
> ------------------------------------------------------
>
>
>
>
>
>
>
> On 9/10/15, 10:23, "Michael Shokhen" <michael.shokhen.biu.ac.il> wrote:
>
>> Dear Amber List users,
>>
>>
>> I now how write a cpptraj script for the generation of average protein
>> structure from
>>
>> MD simulation in one directory as for instance:
>>
>>
>> cpptraj
>> parm ../sm.prmtop
>> trajin ../3_/sm_md3.mdcrd 1001 2000
>> strip :WAT
>> strip :Cl-
>> rms first .C,CA,N
>> average average.pdb PDB
>> run
>>
>>
>> Unfortunately, I don't know how to write a cpptraj script for time
>> interval
>>
>> that covers the border between two sequential directories of continuous
>> MD simulation like in the task described below.
>>
>>
>> I have ran productive MD simulation of my protein
>>
>> in two sequential time intervals 20ns (2000 snapshots) in directory 3_,
>>
>> and then continuing simulation of 20ns (2000 snapshots) in directory 4_.
>>
>> As a result I have in total 40ns (4000 snapshots) MD simulation.
>>
>> I want to generate average 3D structure of my protein on the last 30 ns
>>
>> (3000 snapshots) time interval that includes a border between two
>> sequential MD simulations.
>>
>>
>> What should be a cpptraj script for this case?
>>
>>
>> Thank you,
>>
>> Michael
>>
>>
>>
>>
>> *****************************
>> Michael Shokhen, PhD
>> Associate Professor
>> Department of Chemistry
>> Bar Ilan University,
>> Ramat Gan, 52900
>> Israel
>> email:
>> shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b
>> 9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Sep 10 2015 - 06:00:05 PDT
