Hi,
On Thu, Jul 6, 2023 at 11:59 PM Jing Qu <jqu2.ncsu.edu> wrote:
>
> Hi,
>
> How do the nastruct determine the base pairing? Or how do I change the base pairing criteria?
This is all explained in the 'nastruct' entry in the cpptraj section
of the Amber manual (or the cpptraj manual):
"Base pairs are determined either once from the first frame or from a reference
structure, or can be determined each frame if allframes is specified. Base
pairing is determined first by base reference axis origin distance,
then by stagger,
then by angle between base Z axes, then finally by hydrogen bonding (at least
one hydrogen bond must be present). Base pair parameters will only be written
for determined base pairs."
> Should I try to find an "ideal" structure as a reference?
This might be your best bet.
> When I use the 'allframes' keyword, It will show one base paired with several bases at the same time, like (2,3), (2,15), (3,15), (3,16), (4,15). There is a bit of a mess. And I am hoping they correspond simply one to another, in order.
Without seeing your system, I can't determine whether the default base
pairing criterion is failing or if you have a very strange system. If
you want to send me off-list your topology and a few trajectory frames
I can look at it directly.
-Dan
>
> Best,
> Jing
>
> On Thu, Jul 6, 2023 at 7:42 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> Hi,
>>
>> On Thu, Jul 6, 2023 at 1:48 AM Jing Qu <jqu2.ncsu.edu> wrote:
>> > I installed the version V6.19.5 (GitHub) OpenMP. As I have a parallel strand DNA with 24 residues, ideally I want the base pair parameters for every base pair, like (1, 13), (2, 14), ..., (12, 24). But actually I got only several base pairs for shear, stretch, stagger, buckle, prop, open, hb, bp. Using the option "guessbp" or "guessbp bptype para" gives the same result. Using the option "calcnohb" also didn't show all the base pairs. Is there anything I did wrong?
>>
>> By default, 'nastruct' determines base pairing using the first frame
>> as a reference. My guess is that your first frame may not have all
>> base pairs present according to the default base pairing criteria. You
>> can either adjust the base pair criteria, provide a reference
>> structure that contains all desired base pairing, or use the
>> 'allframes' keyword to determine base pairs for each individual frame.
>> The 'allframes' option may be the simplest one.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> >
>> > Best,
>> > Jing
>> >
>> > On Fri, Jun 30, 2023 at 2:28 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> >>
>> >> Hi,
>> >>
>> >> You only need HIP if you want to run cpptraj on AMD GPUs (just like
>> >> you only need CUDA if you want to run on NVIDIA GPUs). Really the
>> >> "core" of what you need is NetCDF and BLAS/LAPACK (and maybe FFTW if
>> >> you want the PME functionality).
>> >>
>> >> './configure --buildlibs gnu && make install' should be able to
>> >> provide a functioning executable for you with (hopefully) minimal
>> >> fuss.
>> >>
>> >> Good luck,
>> >>
>> >> -Dan
>> >>
>> >> On Fri, Jun 30, 2023 at 1:13 PM Jing Qu <jqu2.ncsu.edu> wrote:
>> >> >
>> >> > Hi,
>> >> >
>> >> > Thank you all for answering my questions. There's one more question about installing. In the GitHub it says for full functionality, CPPTRAJ makes use of a list of libraries. One is HIP. How to get and install it if my system doesn't have it?
>> >> >
>> >> > Best,
>> >> > Jing
>> >> >
>> >> > On Thu, Jun 29, 2023 at 8:58 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> >> >>
>> >> >> Your best bet is to install the GitHub version:
>> >> >> https://github.com/Amber-MD/cpptraj
>> >> >>
>> >> >> You can also install AmberTools 23, which has an updated version of
>> >> >> cpptraj: https://ambermd.org/GetAmber.php#ambertools
>> >> >>
>> >> >> -Dan
>> >> >>
>> >> >> On Mon, Jun 26, 2023 at 11:57 PM Jing Qu <jqu2.ncsu.edu> wrote:
>> >> >> >
>> >> >> > Hi,
>> >> >> >
>> >> >> > On one computer the version is V18.01, another one is V5.1.0. Neither one is okay, is it? By the way, how to upgrade the cpptraj?
>> >> >> >
>> >> >> > Thanks,
>> >> >> > Jing
>> >> >> >
>> >> >> > On Mon, Jun 26, 2023 at 8:51 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> >> >> >>
>> >> >> >> Hi,
>> >> >> >>
>> >> >> >> What version of cpptraj are you using? If it's before version 6.18.0
>> >> >> >> you should upgrade - base pair detection has been greatly improved
>> >> >> >> since then (see https://github.com/Amber-MD/cpptraj/pull/1018).
>> >> >> >>
>> >> >> >> -Dan
>> >> >> >>
>> >> >> >> On Mon, Jun 26, 2023 at 12:36 AM Jing Qu via AMBER <amber.ambermd.org> wrote:
>> >> >> >> >
>> >> >> >> > Dear all,
>> >> >> >> >
>> >> >> >> > I'm using CPPTRAJ to analyze simulations of parallel strand DNA and want to
>> >> >> >> > get step parameters via nastruct. Does anyone know how nastruct identify
>> >> >> >> > the molecule as parallel strands? If I write "guessbp bptype para" in the
>> >> >> >> > nastruct command, the program will simply get stuck and look as if it is
>> >> >> >> > not continuing to run at all. If I just write "guessbp", it would seem to
>> >> >> >> > treat the molecule as anti-parallel. What is the correct way to do that?
>> >> >> >> >
>> >> >> >> > Thanks in advance,
>> >> >> >> > Jing
>> >> >> >> > _______________________________________________
>> >> >> >> > AMBER mailing list
>> >> >> >> > AMBER.ambermd.org
>> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Jul 07 2023 - 08:30:06 PDT
