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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Received on Wed Sep 23 2015 - 01:00:03 PDT
