You can obtain the center of mass of a group of atoms using the 'vector center' command in CPPTRAJ (freely available with AmberTools 14 (http://ambermd.org/AmberTools14-get.html), e.g. 'vector v0 center :1 out v0.dat'.

Distances and angles can be calculated in either PTRAJ or CPPTRAJ with the 'distance' and 'angle' commands, e.g. 'distance d1 :1 :2 out d1.dat', 'angle @1 @2 @3 out angle.dat'. I recommend you review these commands in the Amber 14 manual.

You can obtain the center of mass of a group of atoms using the 'vector center' command in CPPTRAJ (freely available with AmberTools 14 (http://ambermd.org/AmberTools14-get.html), e.g. 'vector v0 center :1 out v0.dat'.

Distances and angles can be calculated in either PTRAJ or CPPTRAJ with the 'distance' and 'angle' commands, e.g. 'distance d1 :1 :2 out d1.dat', 'angle @1 @2 @3 out angle.dat'. I recommend you review these commands in the Amber 14 manual.

Dear Daniel,

Thanks a lot for your kind response.

I have just started to use Amber program. Recently I used Ptraj for my trajectory analysis. So, I have a basic question, since CPPTRAJ is a different command should I used different scripts then? or it is possible to use Ptraj vector action as it is stated on the Amber tools Manual.

So If I understood well, by executing : 'vector v0 center :1 out v0.dat' in CPPTraj I can obtain center of mass of a group of atoms, I have been reviewing the general commans for cpptraj but have not found that four "vector center" is it include in section of e.g center?

Thanks a lot for your help and best regards,

The 'vector' command is described in section 28.11.3 of the Amber 14 manual (in the larger 'Matrix and Vector Actions' section). In general, CPPTRAJ is backwards-compatible with PTRAJ except for the 'hbond' functionality (which is quite a bit easier to use in CPPTRAJ) and 'cluster' functionality (for which not as many clustering algorithms are yet available in CPPTRAJ).

Thanks a lot Dan, I will look for the "vector command" in that section then. So when you say CPPTRAJ is backwards-compatible with PTRAJ means that in most of the cases (except for hbond and "cluster" analysis) I can use the Ptraj scripts I already have?

Yes exactly. A large focus on CPPTRAJ was making it backwards compatible with older PTRAJ scripts. In general if a script is not compatible, CPPTRAJ should print a message to this effect and give you an idea of how to proceed. Good luck!