Dear all,
I used cpptraj in AmberTools 14 to get principal axis and a pseudo trajectory of the vector. I get warning messages in cpptraj and cpptraj processing complete without any errors..
do I need to convert the old topology file and if so what is the utility code to use
ACTION OUTPUT:
Warning: Could not determine atomic number from name [VXYZ]
Warning: : Determining default bond distances from element types.
Warning: Bond length not found for ?? - O, using default= 1.600000
Writing topology 0 () to 'px-rot.prmtop' with format Amber Topology
Writing 'px-rot.mdcrd' as Amber Trajectory
-------------------------------------------------------------------------------------
my cpptraj input is:
parm ../myos_stripwat-4anew4.prmtop
trajin ../myos_wat-4anew4_md3-8.mdcrd 1 10 1
principal :1-155 dorotation out eigen-rot.dat
trajout myos-rot.mdcrd
vector v1 :1-155 principal x out vector_PX-rot.dat
vector v2 :1-155 principal x trajout px-rot.mdcrd parmout px-rot.prmtop
many thanks
Fatima
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Received on Mon Apr 27 2015 - 07:30:03 PDT
