Dear Amber community,
We're using AmberTools13.26 and we find that the atomic number for GAFF
atom type cl is 6 rather than 17 in prmtop file,
which was reported by other users before in the mail list. Has this error
been fixed in the latest release of AmberTools(version 14 or 15)?
We want to conduct GB calculation for our system and the RADII(we are
using modified bondi radii) section within prmtop file indicates
a value of 1.70 for GAFF atom type cl as well as some GAFF atom types for
carbon( such as c3, cc, etc.). Several related sections within prmtop file
are pasted here:
-------------------prmtop file---------------------------
%FLAG
ATOMIC_NUMBER
%FORMAT(10I8)
6 16 8 8 7 6 1 6
6 1
1 6 1 1 1 6 6 6
6 1
6 1 1 1 6 1 1 1
6 1
1 6 1 1 1
%FLAG
AMBER_ATOM_TYPE
%FORMAT(20a4)
cl ss os o n c3 h1 cc c3 h1 h1 c3 hc hc hc cc cd c cd
h4
c3 hc hc hc c3 hc hc hc c3 h1 h1 c3 h1 h1 h1
%FLAG
RADIUS_SET
%FORMAT(1a80)
modified Bondi radii
(mbondi)
%FLAG
RADII
%FORMAT(5E16.8)
1.70000000E+00 1.80000000E+00 1.50000000E+00 1.50000000E+00
1.55000000E+00
1.70000000E+00 1.30000000E+00 1.70000000E+00 1.70000000E+00
1.30000000E+00
1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00
1.30000000E+00
1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00
1.30000000E+00
1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00
1.70000000E+00
1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
1.30000000E+00
1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00
1.30000000E+00
%FLAG
SCREEN
%FORMAT(5E16.8)
8.00000000E-01 9.60000000E-01 8.50000000E-01 8.50000000E-01
7.90000000E-01
7.20000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01
8.50000000E-01
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01
7.20000000E-01 7.20000000E-01 7.20000000E-01 7.20000000E-01
8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
7.20000000E-01
8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01
8.50000000E-01
-------------------prmtop file---------------------------
In modified bondi radii set, what are the actual radii values for Cl
and C? Is that value 1.70 indeed?
We try to conduct post-minimization with implicit solvent model using
GBSA. Will the current atomic number and radius of Cl
disturb the GB calculation? Our control file is as follows:
-----------------control file----------------
&cntrl
MAXCYC =
10000,
ncyc =
1000,
NTPR =
5000,
NTB=0,
IMIN =
1,
igb =
1,
gbsa=1,
cut =
9999
&end
-----------------control file-----------------
And we've noticed that LCPO warning is displayed in output file of the
calculation decribed above:
Unusual nbond for C : 1 1
Using default carbon LCPO parameters
Unusual nbond for C : 12 1
Using default carbon LCPO parameters
Unusual nbond for C : 21 1
Using default carbon LCPO parameters
Unusual nbond for C : 25 1
Using default carbon LCPO parameters
Unusual nbond for C : 32 1
Using default carbon LCPO parameters
I really appreciate it if you could provide some information about these
issues! Thanks!
Best Regards!
Renlong
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Received on Mon Jul 20 2015 - 07:00:02 PDT
