Hello,Amber community
I want to use amoeba force field to run MD with AMBER14,but I wonder if there is something wrong with my prmtop file.
A DNA pdb file was prepared with tleap command in AMBER14.
like this:
tleap -s -f leaprc.ff99bsc0
B=loadpdb ***
check B
solvatebox B TIP3PBOX 8.0
addions B Na+ 0
savepdb B B.pdb
I wrote down the box information(a-axis,b-axis,c-axis) for the Key file.
Next,I used pdbxyz in tinker6.3v to convert it into B.xyz and used B.xyz to reproduce a new pdb file B.pdb_2 as the input of tinker_to_amber.
The key file :
paramters ***/amoebabio09
a-axis ***
b-axis ***
c-axis ***
Then,analyze was used to produce B.analout:
analyze B PC > B.analout
In B.analout,I replaced multipole type "None" with "Z-then-X".
Finally,I used tinker_to_amber to produce inpcrd and prmtop files:
tinker_to_amber -name B -title "B Amoeba FF"
In the prmtop file,I found that numbers are zero under the "FLAG CHARGE" term.
I wonder what's wrong with my job in the course.
Thank you very much
Guowei
2014-09-19
m13654940810
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Received on Thu Sep 18 2014 - 18:30:02 PDT
