AMBER Archive (2007)

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

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Fri Jan 05 2007 - 09:11:43 CST

add includeself in your input file, for example:
 
 hbond series h1 out hbond.dat includeself
 
 I hope it helps.
 
 Cheers,
 
 
lily ferreira <lily_1_mart_at_yahoo.fr> wrote: Hello,

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

De : Jianyin Shao

À : amber_at_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_at_O1

| acceptor mask :MTS_at_N1 :MTS_at_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_at_C1,C2,C3,C4,C5

donor mask :MTS_at_O1

acceptor mask :MTS_at_N1 :MTS_at_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_at_O1

Mask [:MTS_at_O1] represents 1 atoms

PTRAJ: acceptor mask :MTS_at_N1 :MTS_at_H7

Mask [:MTS_at_N1] represents 1 atoms

Mask [:MTS_at_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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