AMBER Archive (2005)

Subject: Re: AMBER: Problem when converting AMBER trajectories to CHARMM format

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Sat Apr 23 2005 - 18:33:48 CDT

> Now I want to convert the trajectories generated by AMBER to CHARMM format to
> some other analysis. Following is my ptraj input file for conversion:
...
> READING TRAJECTORY FROM UNIT 21
> NUMBER OF COORDINATE SETS IN FILE: 0
> NUMBER OF PREVIOUS DYNAMICS STEPS: 0
> FREQUENCY FOR SAVING COORDINATES: 0
> NUMBER OF STEPS FOR CREATION RUN: 0
>
> ***** ERROR ***** NO. OF ATOMS DO NOT MATCH 26796********
> *** LEVEL -4 WARNING *** BOMLEV IS -1
> BOMLEV HAS BEEN SATISFIED. TERMINATING.

I do not believe I ever tried going from AMBER->CHARMM for direct
conversion and readability in CHARMM-- for the very reason that it would
likely be tricky to get a prmtop and PSF to have consistent atom order
throughout... I think that to get this to perform correctly will require
some work since (without having read in a CHARMM trajectory previously
into ptraj) it is not obvious if we have all the information we need to
write one out (i.e. converting a CHARMM from big to little endian works,
but I don't know about AMBER->CHARMM at present).

If you really want to do this, it will require trying to figure out the
code for writing the CHARMM trajectory and getting a PSF in the same
order. It may be easier to get CHARMM to read in generated PDBs and use
these to create a trajectory within CHARMM. It is also possible to get
CHARMM to read in AMBER trajectories directly I believe by using the
read coor universal. Again, you will have to have the correct atom
order for this to make any sense.

We have intended to get this to work along with creating some sort of
prmtop->PSF converter, however it is a tricky problem...

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