I see. I should probably default to Amber topology format if the
extension isn't recognized. Thanks for the report!
-Dan
On Fri, Oct 13, 2017 at 11:48 AM, Li, Wen <wl2290.cumc.columbia.edu> wrote:
> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> 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
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Received on Fri Oct 13 2017 - 10:00:02 PDT
