also, if you strip water, you might want to use the "nobox"
flag after trajout so that box coordinate are not written. by default
they are. if you use the correct prmtop corresponding to the
stripped system, try loading the trajectory in VMD using the
coordinates with box and see if it helps. there is lots of
discussion of this in the archives.
On Sun, Jun 8, 2008 at 2:58 PM, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
> On Sun, Jun 8, 2008 at 11:40 AM, Francesco Pietra <chiendarret.gmail.com> wrote:
>> With Amber10, on accumulating ns of trajectory, I am facing a problem
>> of trajectory analysis unresolved since Amber9 for the same protein
>> and environment, though for a different ligand.
>>
>> The system is a large protein, carrying a large non-peptidic ligand.
>> It is embedded in a POP, TIP3P hydrated, membrane. Everything flows
>> correctly, 39% faster with pmemd with respect to sander.MPI.
>>
>> What I am trying to do with ptraj is combining *.mdcrd while stripping WAT
>>
>> While a complete action would be:
>>
>> trajin prod1.mdcrd.gz
>> trajin prod2.mdcrd.gz
>> ......................
>> trajout prod1-#_no_wat.mdcrd nobox
>> strip :WAT
>> strip :POP
>>
>> I tried simply:
>>
>> trajin prod1.mdcrd.gz
>> trajin prod2.mdcrd.gz
>> ......................
>> trajout prod1-#_no_wat.mdcrd
>> strip :WAT
>>
>> That in view of using the *.prmtop for MD and in order not to change
>> the residue numbering.
>>
>> With the same *.prmtop used for MD, the combined file does not load
>> cleanly with VMD. As expected.
>
> What exaclty do you mean by "not load cleanly"? Do you get any error
> messages? Anyways, I'm not sure it could ever load correctly, since
> after stripping the waters the number of atoms in the prmtop file is
> different than in the prod1-#_no_wat.mdcrd file.
>
>> I removed all WAT from *.prmtop. The same problem.
>
> I suppose there's more to it than just removing the "WAT" residues.
> You may want to take a look into the 'rdparm' utility, described
> together with ptraj. (Check the "stripwater" and then "writeparm"
> commands).
>
> Gustavo.
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Received on Wed Jun 11 2008 - 06:07:14 PDT
