Re : AMBER: intra-molecular h-bonds in ptraj

From: lily ferreira <>
Date: Fri, 5 Jan 2007 13:37:52 +0000 (GMT)


----- Message d'origine ----

De : Jianyin Shao <>

À :

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
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