VMD-L Mailing List

From: Ramya Narasimhan (varsharamya_at_gmail.com)
Date: Sun Dec 19 2010 - 23:40:19 CST

On Thu, Dec 16, 2010 at 10:51 AM, Ramya Narasimhan <varsharamya_at_gmail.com>wrote:

> Hi,
> I used C33b2 version of charmm, its 64-bit. I have attached the copy of
> dcd and psf file and even the output file of charmm. I used charmm22 ff. Its
> just the trial run of 100 frames. Can you figure out the error if any in it?
>
> Thanks in advance for any comments/suggestions.
> Ramya.L.
>
> On Thu, Dec 16, 2010 at 3:55 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>>
>> Hi,
>> The output you got from the DCD plugin indicates that your
>> trajectory file isn't written according to any of the normal
>> DCD file formatting conventions. What exact version of CHARMM
>> wrote the file, and how was it compiled?
>> (32-bit or 64-bit, little endian or big endian CPU, etc)
>> Please send me a copy of a small gzipped version of your
>> CHARMM MC trajectory file along with your structure files
>> and I'll have a closer look at it.
>>
>> Cheers,
>> John
>>
>> On Wed, Dec 15, 2010 at 12:11:46PM +0530, Ramya Narasimhan wrote:
>> > I have a MC trajectory file which is an output from CHARMM. I can't
>> load
>> > the dcd file in the VMD. It is giving an error as
>> >
>> > dcdplugin) unrecognized DCD header:
>> > dcdplugin) [0]: -1543503872 [1]: 1146244931
>> > dcdplugin) [0]: 0xa4000000 [1]: 0x44524f43
>> > dcdplugin) read_dcdheader: corruption or unrecognized file structure
>> > ERROR) Could not read file /home/ramya/charmm-mc/mc1.dcd
>> >
>> > I checked in CHARMM the way of writing trajectory and it seems to be
>> ok. I
>> > removed the DCD header using fixdcd, but still it is not opening in
>> VMD.
>> > Can it be loaded in VMD?
>> >
>> > Thanks in advance for any comments/suggestions.
>> > --
>> > Ramya.L.
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
>> Fax: 217-244-6078
>>
>
>
>
> --
> Ramya.L.
> 

-- 
Ramya.L.