Amber users:
I have Amber7 on a PC with Linux RH7.1, compiled with Machine.g77
I have 2 problems with adding torsions in Xleap
1) If I load Xleap, call up the parm99 proper or improper torsion
parameters, make ZERO changes, and try to save, it complains:
xleap -s -f leaprc.ff99
edit parm99 > Proper Torsion Parameters > Table > Save
"The table is not correct!! Do you really want to save the
table?"
It seems like "../src/leap/src/leap/xaImproperParmTable.c" line 201
does not like "?" as an alphabetic character
2) I tried to perturb GLU+dummy atom to GLH, i.e in the Carboxyl
group, i.e.
type O2 > O
type O2 > OH
dummy atom > HO
Leap checks that the multiple torsions in the unperturbed state map one
to one with the torsions in the perturbed state
However even when I add all the dummy torsions is asks for, all the
errors go away EXCEPT one.
saveamberparmpert GLU prm crd
*** Proper torsion parameters missing ***
atom names: HG2-CG-CD-OE1
atom types: HC-CT-C-O2 =pert=> HC-CT-C-O
Please add a dummy parameter of multiplicity 2
for the pert types to your parameter set.
- e.g. HC-CT-C-O 1 0.0 0. 2.
(This is because multiple torsional potentials may apply to a
single torsion, and each is perturbed individually in gibbs.)
Perhaps there is something wrong with the logic in
.../src/leap/src/leap/unitio.c line 2243 ??
Thanks in advance for feedback/fixes
Andrew Petersen
Received on Tue May 20 2003 - 16:53:01 PDT
