Hi,
Glad to hear it's working. I do want to emphasize that this segfault
only occurs in the unpatched version of cpptraj (V1.0.5). Bugfix 1 for
AmberTools 1.5 corrects this problem
(
http://ambermd.org/bugfixesat.html). I recommend that you apply all
the AmberTools 1.5 bugfixes
(
http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all) since this can
help prevent problems from popping up in the future. If you have
problems applying the patch, let me know.
-Dan
On Tue, Sep 20, 2011 at 1:57 AM, Praapti Jayaswal <praapti.gmail.com> wrote:
> Dear Dan,
>
> I tried running cpptraj using 'nobox' keyword with the trajout command' . It
> works perfectly without segfault!!
>
> Thank you very much!
>
> Praapti
>
> On Fri, Sep 16, 2011 at 10:40 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> >From your output I can see a couple of problems:
>>
>> > CPPTRAJ: Trajectory Analysis. V1.0.5
>>
>> Version 1.0.5 is the unpatched version of cpptraj. The latest version
>> after applying all AmberTools 1.5 bugfixes
>> (http://ambermd.org/bugfixesat.html) should be V1.1.1.
>>
>> > INPUT: Reading Input from file ptraj_res_rmsd.in
>> > [trajin wt1mg_dry.mdcrd]
>> > Warning: Box coords detected in trajectory but not defined in topology!
>> > Setting box type to rectangular.
>>
>> Your input trajectory (wt1mg_dry.mdcrd) contains box coordinates, but
>> your topology (wt1mg_dry.prmtop) does not. To avoid printing box
>> information in your output trajectory when stripping solvent use the
>> 'nobox' keyword with the trajout command.
>>
>> > [reference wt1mg-ref.pdb]
>> > Warning: wt1mg-ref.pdb: Atom 10 name [HG ] does not match parm name [HSG
>> ]
>> > ERROR: PDBfile::SetupRead(): No frames read. atom=2380 expected 2381.
>> > ERROR: Setting up wt1mg-ref.pdb for read.
>>
>> It appears that your reference PDB does not contain the same number of
>> atoms as your input topology (wt1mg_dry.prmtop). You can just use the
>> PDB file as its own topology file, e.g.
>>
>> parm wt1mg-ref.pdb
>> reference wt1mg-ref.pdb parm wt1mg-ref.pdb
>>
>> This will direct cpptraj to read wt1mg-ref.pdb as a reference using
>> parameters obtained from wt1mg-ref.pdb rather than the first topology
>> file. Take care however that any atoms you specify in your mask
>> correspond to atoms in your reference. If necessary, you can specify a
>> separate reference mask for the rms command (and the perres
>> functionality) - see the AmberTools manual for details.
>>
>> So to summarize the above comments, first upgrade your AmberTools
>> installation, consider re-stripping your trajectory with the 'nobox'
>> keyword, and try using the following cpptraj input (adding a reference
>> mask and 'refrange' argument to the rms action if necessary):
>>
>> trajin wt1mg_dry.mdcrd
>> parm wt1mg-ref.pdb
>> reference wt1mg-ref.pdb parm wt1mg-ref.pdb
>> rmsd :1-154 reference perres range 1-154 perresout all-back.tmp
>> perresmask .CA,C,O,N
>>
>> -Dan
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue Sep 20 2011 - 04:30:03 PDT
