Hello AMBER experts,
I am attempting to load the new chi parameters by Zgarbová, et al. (J.
Chem. Theory Comput., 2011, 7 (9), pp 2886–2902). I am following
instructions on
http://fch.upol.cz/en/rna_chi_ol/. I am pretty sure
that the parameters loaded correctly, but I want to verify this before
I invest 4 months in 12 simulations each :-)
My input file, xleap.ol, is as follows:
source /usr/local/amber/openmpi-intel/amber11/dat/leap/cmd/oldff/leaprc.ff99
source /usr/local/amber/openmpi-intel/amber11/dat/leap/cmd/leaprc.ff99bsc0
loadoff RNA_CI.lib
loadamberprep all_nuc94_ol_bsc0.in
loadamberparams frcmod.ol.dat
mol = loadpdb rna.caau.pdb
solvateoct mol TIP3PBOX 8.65
addions mol Na+ 0
saveAmberParm mol prmtop inpcrd
quit
However, this produces the errors:
1)
Warning: per-line charges being overridden by CHARGE block in
D-ADENOSINE - with 5' - OH end group and 3' - O(minus)
Warning: per-line charges being overridden by CHARGE block in
D-ADENOSINE - with 5' - phosphate group and 3' - O(minus) group
Warning: per-line charges being overridden by CHARGE block in
D-ADENOSINE - with 5' - phosphate group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
D-ADENOSINE - with 5' - OH group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
R-ADENOSINE - with 5' - OH end group and 3' - O(minus)
Warning: per-line charges being overridden by CHARGE block in
R-ADENOSINE - with 5' - phosphate group and 3' - O(minus) group
Warning: per-line charges being overridden by CHARGE block in
R-ADENOSINE - with 5' - phosphate group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
R-ADENOSINE - with 5' - OH group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
D-THYMINE - with 5' - OH end group and 3' - O(minus)
Warning: per-line charges being overridden by CHARGE block in
D-THYMINE - with 5' - phosphate group and 3' - O(minus) group
Warning: per-line charges being overridden by CHARGE block in
D-THYMINE - with 5' - phosphate group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
D-THYMINE - with 5' - OH group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in R-URACIL
- with 5' - OH end group and 3' - O(minus)
Warning: per-line charges being overridden by CHARGE block in R-URACIL
- with 5' - phosphate group and 3' - O(minus) group
Warning: per-line charges being overridden by CHARGE block in R-URACIL
- with 5' - phosphate group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in R-URACIL
- with 5' - OH group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
D-GUANOSINE - with 5' - OH group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
R-GUANOSINE - with 5' - OH end group and 3' - O(minus) group
Warning: per-line charges being overridden by CHARGE block in
R-GUANOSINE - with 5' - phosphate group and 3' - O(minus) group
Warning: per-line charges being overridden by CHARGE block in
R-GUANOSINE - with 5' - phosphate group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
R-GUANOSINE - with 5' - OH group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
D-CYTOSINE - with 5' - OH end group and 3' - O(minus) group
Warning: per-line charges being overridden by CHARGE block in
D-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group
Warning: per-line charges being overridden by CHARGE block in
D-CYTOSINE - with 5' - phosphate group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
D-CYTOSINE - with 5' - OH group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
R-CYTOSINE - with 5' - OH end group and 3' - O(minus) group
Warning: per-line charges being overridden by CHARGE block in
R-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group
Warning: per-line charges being overridden by CHARGE block in
R-CYTOSINE - with 5' - phosphate group and 3' - OH group
Warning: per-line charges being overridden by CHARGE block in
R-CYTOSINE - with 5' - OH group and 3' - OH group
I can't find a reference to this on the AMBER mailing list archives.
2) A 3-year old email on
http://structbio.vanderbilt.edu/archives/amber-archive/2008/3972.php
says that this is "innocuous".
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C4-C5-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C6-C5-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-N1-C6-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-N1-C6-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
3) Residues lacking connect0/connect1 -
these don't have chain types marked:
An email by Bill Ross says this is fine:
http://structbio.vanderbilt.edu/archives/amber-archive/2009/3742.php
Output from rdparm, dihedral :1.N1 gives:
247: 1.225 2.57 1.0 :1.O4' :1.C1' :1.N1 :1.C6 (8,9,11,12)
E 248: 1.635 0.29 2.0 :1.O4' :1.C1' :1.N1 :1.C6 (8,9,11,12)
E 249: 0.937 3.24 3.0 :1.O4' :1.C1' :1.N1 :1.C6 (8,9,11,12)
E 250: 0.310 0.56 4.0 :1.O4' :1.C1' :1.N1 :1.C6 (8,9,11,12)
which is different than the standard rna99 parameters
259: 2.500 0.00 1.0 :1.O4' :1.C1' :1.N1 :1.C6 (8,9,11,12)
E 260: 0.000 0.00 2.0 :1.O4' :1.C1' :1.N1 :1.C6 (8,9,11,12)
,which also produces differences between :2.C5' in both residues, so I
am pretty confident it loaded properly, but I would like to verify
this before such a massive time investment.
Thanks for your expertise!
-Dave
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Received on Fri Sep 23 2011 - 06:30:05 PDT
