Cpptraj can handle analyzing trajectories corresponding to different
topologies in the same run. E.g.
parm topo1.parm7
trajin traj1.nc parm topo1.parm7
parm topo2.parm7
trajin traj2.nc parm topo2.parm7
strip <common mask>
<other analysis commands>
-Dan
On Mon, May 14, 2018 at 8:17 AM, Chetna Tyagi <cheta231.gmail.com> wrote:
> Thank you for your reply.
>
> To analyse trajectories using cpptraj, .prmtop files are a requirement. So,
> how can I combine various trajectories that were generated from different
> prmtop files?
>
> Is it possible to strip the .prmtop to contain only the peptide information
> and then load all stripped trajectories ?
>
>
>
>
>
>
>
> On Mon 14 May, 2018, 2:09 PM David A Case, <david.case.rutgers.edu> wrote:
>
>> On Mon, May 14, 2018, Chetna Tyagi wrote:
>> >
>> > I have carried out different simulations of the same peptide with
>> classical
>> > MD and accelerated MD. The parameter files that I used for these were
>> > different.
>> >
>> > Similarly, in chloroform solvent, I have used two different parameter
>> files
>> > for some reason.
>> >
>> > Is it possible to strip the solvent from parameter files and combine
>> these
>> > trajectories to analyze only the peptide and project it on the same PCA
>> > landscape?
>>
>> Yes: PCA analysis doesn't depend on the force field parameters which
>> were used in the underlying trajectory: it just analyzes the
>> fluctuations in coordinates. So, if all the stripped trajectories have
>> the same number of atoms (in the same order), you should be fine.
>>
>> Of course, if the force fields differ in significant ways, it may be
>> difficult to interpret the results you obtain.
>>
>> ....dac
>>
>>
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Received on Mon May 14 2018 - 06:30:04 PDT
