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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Received on Mon Jul 24 2017 - 05:00:04 PDT
