Thank You.I'll definitely follow your suggestion.
Martina
On Wed, Sep 23, 2015 at 4:41 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You are using ptraj-specific command syntax, but your output indicates your
> are using cpptraj to run it. The hbond command is one of the few commands
> that has a different syntax in cpptraj (see the Amber 15 manual page 573:
> 29.9.25 hbond for full details). Also note that cpptraj defines a hydrogen
> bond donor as X-H, where X is the heavy atom. Last, make sure you are using
> an up to date version of cpptraj (15). Hope this helps,
>
> -Dan
>
> On Wednesday, September 23, 2015, Martina Devi <martinadevi2011.gmail.com
> <javascript:_e(%7B%7D,'cvml','martinadevi2011.gmail.com');>> wrote:
>
> > Dear Amber-Users
> >
> > I want to calculate the hydrogen bonding between base-pairs such as
> between
> > Guanine and Cytosine using ptraj where I used the following input:
> >
> > trajin CCC-GGG_md1.mdcrd
> > donor RC O2 N3 N41
> > donor RC3 O2 N3 N41
> > donor RC3 O2 N3 N41
> > acceptor RG3 H21 H11 O6
> > acceptor RG H21 H11 O6
> > acceptor RG H21 H11 O6
> > hbond distance
> >
> > I got the following error in the log file:
> > BEGIN TRAJECTORY PROCESSING:
> > .....................................................
> > PARM [CCC-GGG_wat.prmtop]: Setting up 1 actions.
> > 0: [hbond distance 3.000 Angle 135.000]
> > CCC-GGG_wat.prmtop: Setting up 4412 bonds.
> > Warning: Valence not found for for [Na+ ], using max valence (7)
> > Warning: Valence not found for for [Na+ ], using max valence (7)
> > Warning: Valence not found for for [Na+ ], using max valence (7)
> > Warning: Valence not found for for [Na+ ], using max valence (7)
> > Set up 1464 acceptors:
> > Set up 2829 donors:
> > ----- [CCC-GGG_md1.mdcrd] (1-40, 1) -----
> > 0% 10% 21% 31% 41% 51% 62% 72% 82% 92% 100% Complete.
> >
> > Read 40 frames and processed 40 frames.
> >
> > ACTION OUTPUT:
> >
> > DATASETS:
> > There is 1 data set: distance
> > The given system is a nucleic acid do the above given input satisfies
> the
> > criteria for nucleic acid?Is the error because of the parameter file or
> the
> > input script?
> >
> > Thanks in advance
> >
> > Martina
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 23 2015 - 07:30:03 PDT
