PS I found a workaround for the below problem, which is to first use ptraj
to write a pdb file, using the .psf file as "prmtop" and the original .pdb
file as "trajin". Next, I can use ptraj with the new .pdb file as "prmtop"
and the new .pdb file as "trajin" to get the correct distance.
Perhaps the problems all stem from the .psf file not starting with residue
number 1??
--Marc
On 15 September 2011 14:26, Marc van der Kamp <marcvanderkamp.gmail.com>wrote:
> Many thanks for the reply.
> I forgot ptraj can just deal with PSF files or PDB files instead of a
> prmtop!
> That's really great, BUT:
>
> I've tried this with a 'simple' example and I can't get ptraj to output the
> correct distance between to atoms.
> The atomic coordinates for the distance I tested are:
> ATOM 1328 CA GLU 82 5.338 -15.135 0.848 1.00 0.00
> ATOM 3542 CA THR 218 1.905 -18.135 -5.190 1.00 0.00
>
> The correct distance is thus (about): 7.566
>
> I ran ptraj as follows:
> ptraj ionized.psf dist_test.in &> dist_test.out
>
> with dist_test.in containing:
> trajin ionized.pdb
> distance test out dist_test.dat :94.CA :230.CA noimage
>
> dist_test.dat contains the following incorrect distance: 19.847652
>
> As the residue numbering in ionized.psf starts at 13 instead of 1, I also
> tried the equivalent (with the residue numbers in the masks specifying the
> numbering starting from 1):
> trajin ionized_start1.pdb
> distance test out dist_test.dat :82.CA :218.CA noimage
>
> now dist_test.dat contains the following incorrect distance: 14.942543
>
> I tried just writing a PDB with ptraj as well, and that works, i.e. I get
> the same residue numbers and coordinates as specified in the trajin .pdb
> file.
>
> Further relevant information: I'm using ptraj from AmberTools1.5 with
> bugfixes up to bugfix.13
>
> Any insights as to why ptraj is giving me an incorrect distance?
>
> Further, when I tried using the PDB file (ionized.pdb) as prmtop, I got a
> segfault and errors in the ptraj output that indicate it is expecting a
> prmtop instead of a .pdb:
>
>
> Many thanks in advance for any help/insights!
>
> Marc
>
> On 15 September 2011 13:21, Thomas Cheatham <tec3.utah.edu> wrote:
>
>>
>> > As I'd like to use ptraj to analyze someone else's trajectories (run
>> using
>> > X-PLOR .psf files in NAMD), this feature would be really useful for me.
>>
>> ...for much analysis in ptraj you can get away with using a PDB file
>> instead of a prmtop (and/or the .psf). Ptraj "should" handle all PSF
>> files and if not I need to fix it.
>>
>> However, for non-ptraj (i.e. MM-PBSA) then getting CHAMBER working is
>> appropriate (and shouldn't be too hard).
>>
>> --tec3
>>
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>>
>
>
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Received on Thu Sep 15 2011 - 07:30:03 PDT
