Dear all,
I want to perform a simulation with amoebapro13 force field and amoeba
water model using pmemd.amoeba in amber14.
The system is myoglobin, which is placed in a cubic water box using
solvatebox with 2 Cl- ions to neutralize the system.
The correct pdb.xyz file can be generated using pdbxyz.x in tinker-6.3.3.
However, when I move to the next step to generate the .analout file, there
is a error and couldn't generate the correct .analout file.
I checked the input and output files carefully, and found that the error is
caused due to the Cl- ions.
I tested to remove the ions from the pdb file, and the corresponding
correct .analout file can be generated.
So can anybody give me some help in dealing with the system with ions using
tinker ?
Many thanks in advance.
Sincerely,
Ya Gao
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Received on Mon Dec 08 2014 - 09:00:02 PST
