AMBER Archive (2008)

Subject: Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format?

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Tue Aug 19 2008 - 19:43:58 CDT

Thanks for the prompt response.
The .psf is in CHARMM C31B2 format. I checked the file and it did contain the CMAP keyword in the first line. I will try the AmberTools.

Thanks for the time.
Have a nice day. 

----
Jeffrey

 

>Hi Wei,
>
>I believe this is an issue with newer CHARMM psf files that contain the word CMAP on the first line. This should be fixed in AmberTools1.2 so please download and install this version.
>
>All the best
>Ross
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>> Of Wei Huang
>> Sent: Tuesday, August 19, 2008 7:02 AM
>> To: amber_at_scripps.edu
>> Subject: Re: AMBER: How to convert a CHARMM trajectory to AMBER format?
>> 
>> Hi Jeffrey,
>> 
>> What's the format of your psf file? It should be a CHARMM format psf
>> file.
>> 
>> Cheers,
>> Wei
>> On Tue, 2008-08-19 at 19:30 +0800, Jeffrey wrote:
>> > Dear all,
>> >
>> >      I am new to amber. So could someone please tell me how to convert a
>> md trajectory generated in CHARMM to AMBER format? I write the following
>> script.amber, but it doesn't work...
>> > ----
>> > ptraj prot0-10090.psf << EOF
>> > trajin orient0-10090prot.dcd 1000 10090000 1000
>> > trajout amber.traj
>> > EOF
>> > ----
>> >
>> > When run the script by "ptraj script.amber", the following message was
>> displayed:
>> > ---
>> >   \-/
>> >   -/-   PTRAJ: a utility for processing trajectory files
>> >   /-\
>> >   \-/   Version: "AMBER 9.0 integrated" (April 2006)
>> >   -/-   Executable is: "ptraj"
>> >   /-\
>> >   \-/   Error scanning a value: parm->NTOTAT
>> > Error scanning a value: parm->NTYPES
>> > Error scanning a value: parm->NBONH
>> > Error scanning a value: parm->NTHETH
>> > Error scanning a value: parm->JHPARM
>> > Error scanning a value: parm->JPARM
>> > Error scanning a value: parm->NEXT
>> > Error scanning a value: parm->NTOTRS
>> > Error scanning a value: parm->MBONA
>> > Error scanning a value: parm->MTHETS
>> > Error scanning a value: parm->MPHIA
>> > Error scanning a value: parm->MUMBND
>> > Error scanning a value: parm->MUMANG
>> > Error scanning a value: parm->IFPERT
>> > Error scanning a value: parm->NBPER
>> > Error scanning a value: parm->NGPER
>> > Error scanning a value: parm->NDPER
>> > Error scanning a value: parm->MBPER
>> > Error scanning a value: parm->MGPER
>> > Error scanning a value: parm->MDPER
>> > Error scanning a value: parm->IFBOX
>> > Error scanning a value: parm->NMXRS
>> >
>> > ERROR in NAME_COPY: ... EOF encounters on scanning igraph
>> > ----
>> >
>> >
>> > Any suggestion is greatly appreciated.
>> > Thanks very much for the time.
>> >
>> > Have a nice day.
>> >
>> > -------
>> > Jeffrey
>> >
>> >
>> > __________________________________________________
>> > ИЯПьзЂВсбХЛЂГЌДѓШнСПУтЗбгЪЯф?
>> > http://cn.mail.yahoo.com
>> >
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