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
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>
--
-------------------------
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)
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Received on Wed Sep 23 2015 - 04:30:03 PDT
