Re: how to convert dcd files from namd to charmm

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 15 2007 - 15:49:06 CDT

You could use catdcd to put all the dcds together into one before your
analysis; that's probably the best bet.
http://www.ks.uiuc.edu/Development/MDTools/catdcd/
Peter

regafan_at_usc.es wrote:
> I mean the first trajectory (it has 40 frames). I suppose Charmm read
> the "total"
> trajectory I have created with ptraj and asumes that it only has 40
> frames. The total
> frames I have are 1068.
> Do you have any idea of how Charmm can read all the frames?
>
>
>
>
> Citando Peter Freddolino <petefred_at_ks.uiuc.edu>:
>
>> 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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