Hi,
Currently all SASA parameters are hard-coded. If you need to add new
parameters you will have to edit the source code. Check the
SetAtomLCPO() function in Action_Surf.cpp.
I'll make this an issue on GitHub.
-Dan
On Mon, Jul 24, 2017 at 7:34 AM, Garima Singh <garimabioinfo.gmail.com> wrote:
> Dear Amber user,
>
>
> I am using cpptraj for trajectory analysis. when calculating
> SASA using LCPO method for my metalloprotein found this warning
>
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'cd_cdcj7.prmtop' (1 actions):
> 0: [surf :1 out surf1.dat time 0.002]
> LCPO surface area will be calculated for 19 atoms.
> 19 solute atoms.
> Warning: Using carbon SA parms for unknown atom 1061 type Cd2+
> Warning: Using carbon SA parms for unknown atom 1062 type Cd2+
> Warning: Using carbon SA parms for unknown atom 1063 type Cd2+
>
>
> LCPO method does not have the parameters for cadmium ions so it assigns
> carbon SA parameters to compute the SASA. I want to know what kind of
> parameter i need to add and in which file ? kindly give me your valuable
> suggestion.
>
>
>
>
> *Thank You and Best Wishes*
> --
> *Regards*
> Garima Singh
> AcSIR-PhD Fellow
> Biotechnology Division
> Central Institute Of Medicinal And Aromatic Plant
> CSIR-CIMAP
> Lucknow
> garimabioinfo.gmail.com
>
>
>
>
> *INDIA* Please don't print this e-mail unless you really need to. Be Green !
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Jul 24 2017 - 06:00:04 PDT
