Dear sir:
I have used the antechamber to create the mol2 file of the extra adenosine, like:
.<TRIPOS>MOLECULE
CUA
10 11 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 N9 18.5990 -19.4960 5.3630 ne 1 CUA -0.1909
2 C8 19.3170 -18.8260 6.3300 c1 1 CUA 0.2828
3 N7 19.9600 -17.7650 5.8780 nf 1 CUA -0.2314
4 C5 19.6060 -17.7380 4.5490 cf 1 CUA 0.3502
5 C6 19.9440 -16.8540 3.5200 cf 1 CUA -0.0367
6 N6 20.7390 -15.8180 3.7340 n1 1 CUA 0.1932
7 N1 19.4470 -17.0840 2.2870 nf 1 CUA -0.1023
8 C2 18.6510 -18.1390 2.0960 c1 1 CUA 0.4150
9 N3 18.2700 -19.0580 2.9810 ne 1 CUA -0.2641
10 C4 18.7840 -18.7920 4.2030 ce 1 CUA 0.5843
.<TRIPOS>BOND
1 1 2 2
2 1 10 1
3 2 3 2
4 3 4 1
5 4 5 1
6 4 10 2
7 5 6 2
8 5 7 1
9 7 8 2
10 8 9 2
11 9 10 1
.<TRIPOS>SUBSTRUCTURE
1 CUA 1 TEMP 0 **** **** 0 ROOT
Then, I use the tleap to convert the mol2 file to the ff file, which is like:
!index array str
"CUA"
!entry.CUA.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"N9" "ne" 0 1 131072 1 7 -0.190900
"C8" "c1" 0 1 131072 2 6 0.282800
"N7" "nf" 0 1 131072 3 7 -0.231400
"C5" "cf" 0 1 131072 4 6 0.350200
"C6" "cf" 0 1 131072 5 6 -0.036700
"N6" "n1" 0 1 131072 6 7 0.193200
"N1" "nf" 0 1 131072 7 7 -0.102300
"C2" "c1" 0 1 131072 8 6 0.415000
"N3" "ne" 0 1 131072 9 7 -0.264100
"C4" "ce" 0 1 131072 10 6 0.584300
!entry.CUA.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"N9" "ne" 0 -1 0.0
"C8" "c1" 0 -1 0.0
"N7" "nf" 0 -1 0.0
"C5" "cf" 0 -1 0.0
"C6" "cf" 0 -1 0.0
"N6" "n1" 0 -1 0.0
"N1" "nf" 0 -1 0.0
"C2" "c1" 0 -1 0.0
"N3" "ne" 0 -1 0.0
"C4" "ce" 0 -1 0.0
!entry.CUA.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.CUA.unit.childsequence single int
2
!entry.CUA.unit.connect array int
0
0
!entry.CUA.unit.connectivity table int atom1x int atom2x int flags
1 2 2
1 10 1
2 3 2
3 4 1
4 5 1
4 10 2
5 6 2
5 7 1
7 8 2
8 9 2
9 10 1
!entry.CUA.unit.hierarchy table str abovetype int abovex str belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
!entry.CUA.unit.name single str
"CUA"
!entry.CUA.unit.positions table dbl x dbl y dbl z
18.599000 -19.496000 5.363000
19.317000 -18.826000 6.330000
19.960000 -17.765000 5.878000
19.606000 -17.738000 4.549000
19.944000 -16.854000 3.520000
20.739000 -15.818000 3.734000
19.447000 -17.084000 2.287000
18.651000 -18.139000 2.096000
18.270000 -19.058000 2.981000
18.784000 -18.792000 4.203000
!entry.CUA.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
0 0 0 0 0 0
!entry.CUA.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
"CUA" 1 11 1 "?" 0
!entry.CUA.unit.residuesPdbSequenceNumber array int
0
!entry.CUA.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.CUA.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
However, when I use tleap to loadpdb with the command loadoff *.lib, the errors still
> loadoff ala.ff
Loading library: ./ala.ff
> model1=loadpdb 1y26_a.pdb
Loading PDB file: ./1y26_a.pdb
-- residue 84: duplicate [6 C] atoms (total 2)
ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
(same-name atoms are reduced to a single atom)
Unknown residue: A M number: 71 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: A M sequence: 84
Created a new atom named: 9C within residue: .R<A M 84>
Created a new atom named: 8C within residue: .R<A M 84>
Created a new atom named: 7C within residue: .R<A M 84>
Created a new atom named: 5C within residue: .R<A M 84>
Created a new atom named: 6C within residue: .R<A M 84>
Created a new atom named: 1C within residue: .R<A M 84>
Created a new atom named: 2C within residue: .R<A M 84>
Created a new atom named: 3C within residue: .R<A M 84>
Created a new atom named: 4C within residue: .R<A M 84>
total atoms in file: 1509
Leap added 758 missing atoms according to residue templates:
758 H / lone pairs
The file contained 9 atoms not in residue templates
The PDB file is like :
ATOM 1487 O2' G X 83 3.226 6.631 -6.010 1.00 88.10 O
ATOM 1488 C1' G X 83 4.216 6.065 -3.876 1.00 89.43 C
ATOM 1489 N9 G X 83 3.991 5.487 -2.537 1.00 89.66 N
ATOM 1490 C8 G X 83 4.252 6.089 -1.327 1.00 89.52 C
ATOM 1491 N7 G X 83 3.957 5.376 -0.282 1.00 89.03 N
ATOM 1492 C5 G X 83 3.473 4.208 -0.827 1.00 89.02 C
ATOM 1493 C6 G X 83 3.005 3.061 -0.159 1.00 89.27 C
ATOM 1494 O6 G X 83 2.942 2.890 1.064 1.00 89.30 O
ATOM 1495 N1 G X 83 2.590 2.068 -1.054 1.00 89.82 N
ATOM 1496 C2 G X 83 2.629 2.186 -2.432 1.00 89.50 C
ATOM 1497 N2 G X 83 2.185 1.128 -3.130 1.00 89.30 N
ATOM 1498 N3 G X 83 3.069 3.273 -3.071 1.00 89.41 N
ATOM 1499 C4 G X 83 3.479 4.245 -2.208 1.00 89.41 C
TER 1500 G X 83
END
ATOM 1506 N9 CUA M 90 18.599 -19.496 5.363 1.00 36.40 N
ATOM 1507 C8 CUA M 90 19.317 -18.826 6.330 1.00 37.43 C
ATOM 1508 N7 CUA M 90 19.960 -17.765 5.878 1.00 37.14 N
ATOM 1509 C5 CUA M 90 19.606 -17.738 4.549 1.00 37.42 C
ATOM 1510 C6 CUA M 90 19.944 -16.854 3.520 1.00 37.76 C
ATOM 1511 N6 CUA M 90 20.739 -15.818 3.734 1.00 36.15 N
ATOM 1512 N1 CUA M 90 19.447 -17.084 2.287 1.00 36.86 N
ATOM 1513 C2 CUA M 90 18.651 -18.139 2.096 1.00 37.35 C
ATOM 1514 N3 CUA M 90 18.270 -19.058 2.981 1.00 38.33 N
ATOM 1515 C4 CUA M 90 18.784 -18.792 4.203 1.00 37.55 C
How can I fix this ?
Thank you very much
2009-11-04
Zhou Gong
School of Physics
Huazhong University of Science and Technology
Wuhan
Hubei Province
China
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Received on Wed Nov 04 2009 - 07:30:04 PST
