Dear Himanshu,

VMD is fine for visualizing your results (i.e trajectory or static structure), but if you want a statistical analysis of hydrogen bond formation and breaking then use AMBER's ptraj program. Ptraj has the ability to compute the hydrogen bond for any specified donor-acceptor combination. Take a look at the following tutorial: http://ambermd.org/tutorials/basic/tutorial3/section6.htm .

Depending on what structure you are viewing, VMD may draw in a hydrogen bond or not, depending on the default geometric parameters that VMD uses to define a hydrogen bond. Since hydrogen bond are dynamic in nature, and if you are viewing a single structure, then perhaps you are seeing an instance in time where the third hydrogen bond is not stable. This is why you want to analyze the trajectory and do a statistical analysis.

If the third hydrogen bond is statistically not present then perhaps there is an error in the input, or it is indeed a meaningful result that you need to figure out the chemical/physical (e.g. conformationally proghibited) reason why it happens.

Best regards,

K

Dear Himanshu,

VMD is fine for visualizing your results (i.e trajectory or static structure), but if you want a statistical analysis of hydrogen bond formation and breaking then use AMBER's ptraj program. Ptraj has the ability to compute the hydrogen bond for any specified donor-acceptor combination. Take a look at the following tutorial: http://ambermd.org/tutorials/basic/tutorial3/section6.htm .

Depending on what structure you are viewing, VMD may draw in a hydrogen bond or not, depending on the default geometric parameters that VMD uses to define a hydrogen bond. Since hydrogen bond are dynamic in nature, and if you are viewing a single structure, then perhaps you are seeing an instance in time where the third hydrogen bond is not stable. This is why you want to analyze the trajectory and do a statistical analysis.

If the third hydrogen bond is statistically not present then perhaps there is an error in the input, or it is indeed a meaningful result that you need to figure out the chemical/physical (e.g. conformationally proghibited) reason why it happens.

Best regards,

K

I used vmd for simple fluid but output result is not valid.

please check cutoff angle and cut off distance that used as default in VMD. for hydrogen definition cutoff angle must be 30 degree or 150 degree. but in VMD this value is 20!!!????

please see literatures.

Of course it works as long as you have a correct amber topology file.

CPPTRAJ (advance version of PTRAJ) does not know its bio polymer or non-bio polymer.

You need amber topology file typically (.prmtop extension ) file

and coordinate in form of either pdb amber binary or ascii or dcd.

Please do see the Amber manual for details.