Hi,
Yes, unfortunately I haven't yet included the 'previous' functionality
in the cpptraj RMS action, though it will probably be there sometime
in the not too distant future.
-Dan
On Tue, Jun 14, 2011 at 11:38 PM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
> Thanks Dan!
>
> I was wondering about the keyword "previous" from the rms command in ptraj,
> is not available anymore for cpptraj? I have gone through the manual for the
> cpptraj command and this option is not available.
>
> Po
>
>
> On Mon, Jun 13, 2011 at 8:25 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> I presume you are referring to the keywords for the 'rmsd' action. You
>> can specify an external reference structure for an rms command in
>> three different ways:
>>
>> refindex <#>: Use reference structure read in by a previous "reference
>> <filename>" command, where <#> is the order the reference was read in.
>> ref <filename>: Use reference structure read in by a previous
>> "reference <filename>" command.
>> reference: Short for "refindex 0" (first reference structure read in),
>> included for backwards compatibility with ptraj.
>>
>> For example, given the script:
>>
>> trajin mdcrd
>> reference ref1.rst7
>> reference ref2.rst7
>> rmsd reference :1-10 out r1.dat
>> rmsd refindex 1 :1-10 out r2.dat
>> rmsd ref ref2.rst7 :1-10 out r2.dat
>>
>> The first rms command will use ref1.rst7 as a reference, and the last
>> two rms commands will use ref2.rst7 as an index. See the manual for
>> more details. Let me know if you still have questions.
>>
>> -Dan
>>
>>
>> On Mon, Jun 13, 2011 at 6:39 AM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
>> > Hi All,
>> >
>> > Can you clearly elucidate the difference between the keywords "ref" and
>> > "reference" in cpptraj.
>> >
>> > Thanks!
>> >
>> > Po
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Received on Tue Jun 14 2011 - 21:00:04 PDT
