Hi,
The problem is here:
> Error: SetSurfaceInfo(): Parm 1mbn.pdb does not contain bond info.
The LCPO algorithm as it is implemented in Cpptraj requires bond and
atom type information. You will have to create an amber prmtop with
leap in order to calculate LCPO surface area. Cpptraj should handle
the error better however - thanks for the report.
-Dan
2012/3/7 Guillermo Mulliert Carlín <Guillermo.Mulliert.crm2.uhp-nancy.fr>:
> Hello,
> I am triying to use cpptraj to calculate the surface area with the
> command surf in a pdb file (a pdb file downloaded from rcsb). I dowonloaded
> AmberTools 1.5, applied buxfix.all and compiled it with gcc gnu (version
> 4.4.5 (Debian 4.4.5-8)) in a 64 bits system. I am using cpptraj V1.1.2
>
> My input is
> ...............................................................................
> parm 1mbn.pdb
> trajin 1mbn.pdb
> parminfo :1
> surf r1 :1 out sasa.dat
> ...............................................................................
>
> I attached the output. Apparently the program finishes as the output
> prints "Complete" just before "Segmentation fault".
>
> Can anybody help me?
>
> Is the answer that cpptraj cannot compute the surface without
> hydrogens?
>
> Thanking you in advance
>
> Guillermo Mulliert
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Received on Wed Mar 07 2012 - 08:30:02 PST
