Re: how to convert dcd files from namd to charmm

From: regafan_at_usc.es
Date: Thu Mar 15 2007 - 15:34:31 CDT

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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