Respected sir,
Now I understand the reason behind the difference in size and will stick to the file created by cpptraj.
I will try to reframe my question regarding merging prmptop files.
I already have a combined trajectory file and want to do analysis using cpptraj like calculating ligand RMSD , autoimage etc but for that I need to have a pmrtop file. Before the trajectory merging I was uising prmtop of the respective trajectory files like cpptraj 2NL9_complex.prmtop autoimage_nowat > autoimage_nowat.out. However, I am not sure which prmptop file should I use for the analysis of the combined trajectory i.e. anyone of the initial two prmptop files (2NL9_complex.prmtop, 4HW4_complex.prmtop), or both or a combined prmptop file and what will be the syntax.
Thanks and regrds,
Nitin Sharma
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Thursday, March 27, 2014 2:18 AM
To: amber.ambermd.org
Subject: Re: [AMBER] combining trajectories with diff. number of residues for same protein
On Thu, 2014-03-27 at 01:42 +0800, Nitin Sharma wrote:
> Respected sir,
>
> Thanks for prompt reply and yes that solved my problem. Only one more
> query regarding generation of stripped prmtop. As I can generate the
> prmtop files by following two which I can see differs slightly in
> their size. So, which process is the correct approach?
The difference in size stems from a fundamental difference in how cpptraj and ParmEd "compute" a topology file. cpptraj eliminates the entries for each of the stripped atoms in the atom property arrays (like MASS, ATOM_NAME, etc.) and renumbers all of the pointers in the bond, angle, and dihedral arrays (as well as the exclusion lists). It does not, however, trim the bond/angle/dihedral type arrays to eliminate the parameters that are no longer in use. This prevents cpptraj from having to keep track of those types (if you never touch those arrays, then you never have to adjust pointers _into_ that array which simplifies the bookkeeping). I'm not sure if this is still true for Amber14, but Dan can correct me if I'm wrong.
ParmEd, however, recomputes the _entire_ topology file and adds types into the parameter file as they're used. This approach eliminates all unused parameter types and leads, in general, to a smaller topology file than those written by cpptraj. Both are equally valid topology files, however, and result in completely equivalent energies and forces. They look completely different, though, as the pointer and parameter ordering is completely different (but again, equivalent).
>
> cpptraj complex_solvated.prmtop strip2merge_2 > strip2merge_2.out
> #strip2merge2
> trajin 5md.mdcrd 2000 last
> strip :1-18,168-182,Na+,Cl- outprefix stripped_2NL9_046 trajout
> 2NL9_046_strip.mdcrd netcdf nobox
>
> OR
>
> parmed.py complex_solvated.prmtop strip_Parm_2
> #strip_Param_2
> strip :1-18,168-182,Na+,Cl- outprefix stripped_2NL9_046
"outprefix" is not a recognized keyword for ParmEd (in cpptraj it is only used to trigger a prmtop dump, which doesn't apply in ParmEd). In the next version of ParmEd this will be a fatal error by default.
> parmout
> /hpctmp/a0068362/MCL1_combined_test/2NL9_046_strip_prmtop.prmtop
>
> Moreover, as prmtop file is required by cpptraj so do I need to load
> both prmtop files or have to merge prmtop files as well. If I have to
> merge them then how can I do that ?
I'm not sure what you mean by "merge" them. You can use either the topology file written by cpptraj or the one written by ParmEd -- they should both work exactly the same for any program. Since you're already using cpptraj, though, you can easily eliminate ParmEd from your workflow here.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 26 2014 - 13:00:02 PDT
