Hi Dan,
It turned out that it is not computer space issue, but the problem was with my output file extension, which I used newfile.top. Now the output file used name newfile.out or newfile.parm7, all worked. With Ambertools 14, using .top was not a problem.
Thank you!
Wen
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Friday, October 13, 2017 5:25:43 AM
To: AMBER Mailing List
Subject: Re: [AMBER] parmstrip with cpptraj in Ambertools 17
Hi,
Thanks for the file. However I was not able to reproduce your error. I
can strip and write the file with no error using the following input:
parm mut2.top
parmstrip :1-4938
parmwrite out temp.parm7
The original error message seems to indicate the issue is really with
writing the file, not stripping. Check your script to make sure you
are writing to a location where you have write permission and/or that
there is enough space on the device.
-Dan
On Thu, Oct 12, 2017 at 8:35 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Can you send me your topology file off list so I can try to reproduce
> the error? Thanks.
>
> -Dan
>
> On Thu, Oct 12, 2017 at 1:12 PM, Li, Wen <wl2290.cumc.columbia.edu> wrote:
>> Hi Everyone,
>>
>>
>> In the past, cpptraj in Ambertools 14 worked for me for stripping parameter files.
>>
>> The input file (my_input) was:
>>
>>
>> parm mytopo
>>
>> parmstrip :1-69
>> parmwrite out new.top
>> run
>>
>> Now, using cpptraj in Ambertools 17, I did:
>> source $AMBERHOME/amber.csh (on a pre-installed workstation)
>> or source /mypath/ambertools/17/amber.csh (in SBgrid)
>>
>> $AMBERHOME/bin/cpptraj < my_input
>>
>> resulted: Error: writing topology file 'new.top'
>>
>>
>> I noticed there was an email stream on September 1, 2017 with title "Cpptraj and parmwrite and strip" (http://archive.ambermd.org/201709/0019.html), so I am wondering if cpptraj in Ambertools 17 does no longer work for this stripping function.
>>
>> Thank you!
>>
>> Wen
>>
>> Re: [AMBER] Cpptraj and parmwrite and strip from Daniel ...<http://archive.ambermd.org/201709/0019.html>
>> archive.ambermd.org
>> From: Daniel Roe <daniel.r.roe.gmail.com> Date: Fri, 01 Sep 2017 20:27:18 +0000 You must have an old version of cpptraj. I suggest upgrading to at least
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Oct 13 2017 - 09:00:03 PDT
