Dear Dan thanks for the reply.
After your email I looked into strip2merge_1.out and strip2merge_2.out which are the files corresponding to the stripping of the trajectory and the and generating prmtop file related to stripped trajectory. I found out that number of residues are different in both the files. Moreover, the number of residues is way more than what I have in PDB file. For me the term residues is applied to amino acids only. If it different in case of AMBER? I have attached the pdb files and .out files with the email
I have combined both trajectories using their corresponding prmtop files (.out file attached with email) and it was successful thus creating combined_2NL9_4HW4_046.mdcrd. Considering my prmtop files can I combine using the single prmtop file as you have suggested?
Using this combined trajectory I want to cluster the poses of ligand and do other analysis. Will this be correct protocol
cpptraj -i ligand_rmsd > ligand_rmsd.out
#ligand_rmsd
parm stripped_4HW4_046_complex_solvated.prmtop [4hw4]
parm stripped_2NL9_046_complex_solvated.prmtop [2NL9]
trajin combined_2NL9_4HW4_046.mdcrd parm [2NL9] parm [4hw4]
autoimage
reference 2minimize.rst [minxray]
rms .CA,C,N ref [minxray]
rms :UNK nofit out combined20to100ns_ligand_rmsd.dat ref [minxray]
I have added the files in dropbox
https://www.dropbox.com/sh/zb8flt93fd6mn3g/udKtvWMDK3/trajectory
Regards,
Nitin Sharma
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Thursday, March 27, 2014 4:16 AM
To: AMBER Mailing List
Subject: Re: [AMBER] combining trajectories with diff. number of residues for same protein
OK, I think I understand what you are trying to do here, and I think you need to modify your workflow slightly. Have you verified that your combined trajectory has the correct number of frames? In cpptraj, a 'trajout'
command is associated with a specific topology, just like a 'trajin'
command. Output trajectories are only written if the current topology being processed matches the topology it was set up with - this is to prevent e.g.
the number of atoms being written to the trajectory from changing in the middle of a run.
Based on your previous scripts, I'm guessing that the topologies 'stripped_4HW4_046_complex_solvated.prmtop' and 'stripped_2NL9_046_complex_solvated.prmtop' end up having the same number of atoms and residues, correct? Then you can combine the trajectories with either topology like so:
parm stripped_4HW4_046_complex_solvated.prmtop
trajin 4hw4_046_strip.mdcrd
trajin 2NL9_046_strip.mdcrd
trajout combined_2NL9_4HW4_046.mdcrd
You can use either stripped topology for the combining and subsequent processing. Note that this may give odd results however if the residues, connectivity etc are not the same between the two topologies (even if the number of atoms is). If you need to have the specific topologies associated with each system to be active in turn then you should just process the trajectories without combining them, e.g.
parm stripped_4HW4_046_complex_solvated.prmtop [4hw4] trajin 4hw4_046_strip.mdcrd parm [4hw4] parm stripped_2NL9_046_complex_solvated.prmtop [2NL9] trajin 2NL9_046_strip.mdcrd parm [2NL9] < actions >
Hope this helps,
-Dan
On Wed, Mar 26, 2014 at 1:38 PM, Nitin Sharma <sharmanitin.nus.edu.sg>wrote:
> 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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>
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Mar 27 2014 - 01:00:02 PDT
