Hi,
I tried to calculate energy and something else using NAB, but it seems to
have a problem with a metallic ion.
This is my nab code:
#############################
molecule m;
int ier;
float m_xyz[dynamic], f_xyz[dynamic];
float dgrad, fret;
file outfile;
m = getpdb("test.pdb");
allocate m_xyz[3*m.natoms];
allocate f_xyz[3*m.natoms];
readparm(m, "test.prmtop");
outfile = fopen( "nab.out", "w" );
dumpmolecule( outfile, m, 1, 1, 1 );
fclose( outfile );
mm_options("cut=999.0, ntpr=1, nsnb=999, gb=0");
mme_init(m, NULL, "::ZZZZ", m_xyz, NULL);
// Energy
fret = mme( m_xyz, f_xyz, -1 );
printf( "mme returns %f\n", fret );
#############################
The STDOUT I get is:
#############################
Reading parm file (test.prmtop)
title:
MW6
mm_options: cut=999.0
mm_options: ntpr=1
mm_options: nsnb=999
mm_options: gb=0
bond: nan
angle: nan
dihedral: nan
enb14: nan
eel14: nan
enb: nan
eel: nan
egb: 0.000000000
econs: 0.000000000
esurf: 0.000000000
Total: nan
frms: nan
mme returns nan
#############################
Dumped molecule (nab.out):
#############################
Molecule 0x5d28480 {
frame
origin 0.000 0.000 0.000
X-axis 1.000 0.000 0.000
Y-axis 0.000 1.000 0.000
Z-axis 0.000 0.000 1.000
1 strands
Strand 0x5d28510 {
name 1
num 1
slct ---
mol 0x5d28480
next (nil)
nres 1
rsiz 10000
res 0x2b0715531010
Residue 0x5d28570 {
name MW6
resid 1
numid 1
num 1
tnum 1
kind Undef
akind Undef
slct ---
next (nil)
str 0x5d28510
natm 19
atoms 0x5d28600
ATM[ 0, 0,0x5d28600,0x5d28570] MG --- 0.000 0.000 0.000 []
ATM[ 1, 1,0x5d286b0,0x5d28570] O1 --- -1.369 -0.251 -1.580 [ 2 3]
ATM[ 2, 2,0x5d28760,0x5d28570] H11 --- -2.308 -0.397 -1.499 [ 1]
ATM[ 3, 3,0x5d28810,0x5d28570] H12 --- -1.167 -0.239 -2.512 [ 1]
ATM[ 4, 4,0x5d288c0,0x5d28570] O2 --- 1.369 0.251 1.580 [ 5 6]
ATM[ 5, 5,0x5d28970,0x5d28570] H21 --- 1.167 0.239 2.512 [ 4]
ATM[ 6, 6,0x5d28a20,0x5d28570] H22 --- 2.308 0.397 1.499 [ 4]
ATM[ 7, 7,0x5d28ad0,0x5d28570] O3 --- -1.566 -0.216 1.391 [ 8 9]
ATM[ 8, 8,0x5d28b80,0x5d28570] H31 --- -2.107 0.483 1.749 [ 7]
ATM[ 9, 9,0x5d28c30,0x5d28570] H32 --- -1.868 -1.032 1.782 [ 7]
ATM[ 10, 10,0x5d28ce0,0x5d28570] O4 --- 1.566 0.216 -1.391 [ 11 12]
ATM[ 11, 11,0x5d28d90,0x5d28570] H41 --- 2.107 -0.483 -1.749 [ 10]
ATM[ 12, 12,0x5d28e40,0x5d28570] H42 --- 1.868 1.032 -1.782 [ 10]
ATM[ 13, 13,0x5d28ef0,0x5d28570] O5 --- 0.328 -2.079 0.046 [ 14 15]
ATM[ 14, 14,0x5d28fa0,0x5d28570] H51 --- -0.082 -2.731 -0.517 [ 13]
ATM[ 15, 15,0x5d29050,0x5d28570] H51 --- 0.915 -2.548 0.633 [ 13]
ATM[ 16, 16,0x5d29100,0x5d28570] O6 --- -0.328 2.079 -0.046 [ 17 18]
ATM[ 17, 17,0x5d291b0,0x5d28570] H61 --- 0.082 2.731 0.517 [ 16]
ATM[ 18, 18,0x5d29260,0x5d28570] H61 --- -0.915 2.548 -0.633 [ 16]
No external bonds
}
}
}
#############################
One problem I see here is MG does not have any bonded connection. ( ATM[
0, 0,0x5d28600,0x5d28570] MG --- 0.000 0.000 0.000 [] )
However, MG does have bonds. This is bond information read from rdparm
RDPARM MENU: printbond
Mask [*] represents 19 atoms
Bond Kb Req atom names (numbers)
1: 553.00 0.957 :1.O1 :1.H11 (2,3)
2: 553.00 0.957 :1.O1 :1.H12 (2,4)
3: 553.00 0.957 :1.O2 :1.H21 (5,6)
4: 553.00 0.957 :1.O2 :1.H22 (5,7)
5: 553.00 0.957 :1.O3 :1.H31 (8,9)
6: 553.00 0.957 :1.O3 :1.H32 (8,10)
7: 553.00 0.957 :1.O4 :1.H41 (11,12)
8: 553.00 0.957 :1.O4 :1.H42 (11,13)
9: 553.00 0.957 :1.O5 :1.H51 (14,15)
10: 553.00 0.957 :1.O5 :1.H51 (14,16)
11: 553.00 0.957 :1.O6 :1.H61 (17,18)
12: 553.00 0.957 :1.O6 :1.H61 (17,19)
13: 640.00 2.090 :1.MG :1.O1 (1,2)
14: 640.00 2.090 :1.MG :1.O2 (1,5)
15: 640.00 2.090 :1.MG :1.O3 (1,8)
16: 640.00 2.090 :1.MG :1.O4 (1,11)
17: 640.00 2.090 :1.MG :1.O5 (1,14)
18: 640.00 2.090 :1.MG :1.O6 (1,17)
In addition, the calculated energy is also wrong.
I believe there is no problem with the prmtop file because I could
successfully run minimization with sander.
Could anyone suggest how to fix this problem?
--
Best,
InSuk Joung
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Received on Wed Jul 28 2010 - 15:00:03 PDT
