Hi All,
I want to load my pdb file having many waters with solute. I was getting many errors due to water.
So I just tried to loadpdb TP3.pdb having only one water (file attached containing one water molecule; TP3.pdb) as follows
loadamberparams parm99.dat
loadoff solvents.lib
WAT = copy TP3
p = loadpdb TP3.pdb
I get this error
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-H1-O-*
....
....
Error is already discussed in archive with suggestion to source solvents.cmd (http://archive.ambermd.org/200511/0220.html) and if do like this
loadamberparams parm99.dat
loadoff solvents.lib
source solvents.cmd
xleap/tleap quits so I cannot loadpdb
the output solvents.log shows it cannot save box information
BUT if I do using ff03 as:
source leaprc.ff03
p = loadpdb TP3.pdb
No such error (+---Tried to superimpose torsions) comes
So I have two doubts:
1) leaprc.ff03 also loads solvents.lib and parm99.dat for water. No error comes in this case, someone please suggest why so ??
2) if I want just to use parm99.dat and loadoff solvents.lib I should source solvents.cmd, why xleap/tleap quits??
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- X-unknown/x-pdb attachment: TP3.pdb
Received on Thu Dec 15 2011 - 23:30:03 PST
