Hello,
----- Message d'origine ----
De : Jianyin Shao <jyshao2004.gmail.com>
À : amber.scripps.edu
Envoyé le : Jeudi, 4 Janvier 2007, 21h11mn 36s
Objet : Re: AMBER: intra-molecular h-bonds in ptraj
| There might be something wrong with the ptraj's interpretation of the selection command.
|
| Please use
| donor mask :MTS.O1
| acceptor mask :MTS.N1 :MTS.H7
|
| instead of
| donor MTS O1
| acceptor MTS N1 H7
|
| If you cannot fix the problem by doing so, please let me know.
|
| Jianyin
I did as you suggest, my input file is now
trajin file1.mdcrd
rms first out file1.rms :GSU.C1,C2,C3,C4,C5
donor mask :MTS.O1
acceptor mask :MTS.N1 :MTS.H7
hbond distance 10.0 donor acceptor series hbond
I put "distance 10.0" just for test as I know that the atoms involved are at a distance less than 6.0 Angstroms
during the simulation, and the answer is
[...]
"PTRAJ: donor mask :MTS.O1
Mask [:MTS.O1] represents 1 atoms
PTRAJ: acceptor mask :MTS.N1 :MTS.H7
Mask [:MTS.N1] represents 1 atoms
Mask [:MTS.H7] represents 1 atoms"
[...]
"data will be sorted, intra-residue interactions will NOT be included,"
so I still cannot list intra-residue h-bonds.
Have you any other suggestion?
Thanking you in advance
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Received on Sun Jan 07 2007 - 06:07:40 PST
