Re: how to convert dcd files from namd to charmm

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 15 2007 - 15:16:25 CDT

By the "first individual one", do you mean the first frame, or the first
trajectory?

Peter

regafan_at_usc.es wrote:
>
> Hello,
> I have another problem about trajectories from NAMD to be used in the
> analysis with Charmm. With NAMD, the simulation was done by steps, and
> I don´t have only one trajectory file for all the simulation, but
> several files that I have treated with ptraj to get a total
> trajectory. When this trajectory is used in CHARMM, the program only
> recognizes the first individual one, and the loop used in the script
> stops.
> Do you have a solution for doing that Charmm reads all the steps of
> the trajectory?
>
>
> The script for analysis is:
>
> ...
>
> open read card name "top_all22_prot.inp" unit 20
> read rtf card unit 20
> close unit 20
>
> open read card name "par_all22_prot.inp" unit 20
> read parameter card unit 20
> close unit 20
>
> !open and read psf file
> open read card name "4f2hc_rx.psf" unit 20
> read psf card unit 20
> close unit 20
>
> !Set up for reading coordinate sets from trajectory and writing energy
> data
> open write card name "energy.tst" unit 52
> open read file name trayectoria_10ns.dcd unit 51
> trajectory query unit 51
> trajectory iread 51 begin ?start skip ?skip
>
> set i 1
>
> !Loop for reading coordinate sets and calculating an interaction energy.
> label loop
> trajectory read
> update
> interaction select segid pro1 .and. resid 1 : 416 end -
> select segid pro2 .and. resid 417 : 837 end unit 52
> increment i
> if i le ?nfile goto loop
>
> stop
>
> ...
>
> Thank you very much for your help,
>
> Rebeca García
> Post-doctoral student
> Barcelona
> Spain
>
> Citando regafan_at_usc.es:
>
>>
>> Thank you very much, Alessandro.
>> You were right, I had run NAMD on a computer of different endianness of
>> the computer on which I was analyzing the trajectory with Charmm. Now,
>> it works without any format conversion.
>> Thanks!
>>
>> Rebeca García
>> Post-doctoral student
>> Barcelona
>> Spain
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Citando Alessandro Cembran <cembran_at_chem.umn.edu>:
>>
>>> Rebeca,
>>>
>>> I've been running NAMD and post processing the trajectories with CHARMM
>>> as well and I've never run into any problem.
>>> In some cases, one might have to pay attention to the orientation of
>>> the box (I am thinking about hexagonal cells, that need to be rotated
>>> by 15 degrees around the Z axis) but the raw numbers are always read
>>> correctly.
>>> Another thing that I can think of is that you might have run NAMD on a
>>> computer of different endianness of the computer on which you are
>>> analyzing the trajectory. If this is the case, you might
>>> a) Recompile CHARMM with TESTENDIAN in the pref.dat (never tried
>>> this one)
>>> b) Change the endianness of the shell on which you are running CHARMM
>>> to match the original one:
>>> export F_UFMTENDIAN=little or ...=big
>>> c) Compile and run CHARMM on the machine the trajectories have been
>>> produced.
>>>
>>> If none of the two cases applies to your problem, then could you be
>>> more specific about what is the compatibility issue?
>>>
>>> Alessandro
>>>
>>> regafan_at_usc.es wrote:
>>>> Hello,
>>>> I have done a simulation of a protein with NAMD, using the Charmm
>>>> force field, and now I would like to perform an analysis with
>>>> CHARMM.
>>>> I have problems of compatibility of the trajectory files obtained
>>>> with NAMD and CHARMM. Does anyboy knows how to convert a dcd
>>>> trajectory file from NAMD to the correct one used by Charmm?
>>>>
>>>> Thanks a lot!
>>>>
>>>> Rebeca García
>>>> Post-doctoral student
>>>> Barcelona
>>>> Spain
>>>>
>>>>
>>>
>>>
>>> --Alessandro Cembran,PhD
>>> Post Doctoral Associate
>>> Mailing Address:
>>> Univ. of Minnesota, Dept. of Chemistry
>>> G2, 139 Smith Hall 207 Pleasant St SE
>>> Minneapolis, MN 55455-0431
>>> Office:
>>> Univ. of Minnesota, Walter Library
>>> 117 Pleasant St SE, Room 473
>>> Phone: +1 612-624-4617
>>> E-mail: cembran_at_chem.umn.edu
>
>

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