Dear sir:
Have you just modified the TER line in the PDB file ? I have done this like your addivise, like
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
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
END
However, when I use the tleap, new error happened
> CUA=loadmol2 CUA_1.mol2
Loading Mol2 file: ./CUA_1.mol2
Reading MOLECULE named CUA
> model=loadpdb 1y26_a.pdb
Loading PDB file: ./1y26_a.pdb
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-N3-C2-*
+--- With Sp2 - Sp1
+--- 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-C2-*
+--- With Sp2 - Sp1
+--- 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: *-N7-C8-*
+--- With Sp2 - Sp1
+--- 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: *-N9-C8-*
+--- With Sp2 - Sp1
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
total atoms in file: 1509
Leap added 758 missing atoms according to residue templates:
758 H / lone pairs
I'm sending you my pdb file, mol2 file, could you please help me to solve this ?
Thanks for your patient and help
2009-11-05
Zhou Gong
School of Physics
Huazhong University of Science and Technology
Wuhan
Hubei Province
China
发件人： FyD
发送时间： 2009-11-04 23:29:10
收件人： AMBER Mailing List
抄送：
主题： Re: [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber
Dear Zhou Gong,
I slightly modified your PDB file format; see below;
It seems to work - even if hydrogens are not present....
xleap
CUA = loadmol2 CUA.mol2
mol = loadpdb mol.pdb
regards, Francois
mol.pdb:
ATOM 1487 O2' G X 83 3.226 6.631 -6.010
ATOM 1488 C1' G X 83 4.216 6.065 -3.876
ATOM 1489 N9 G X 83 3.991 5.487 -2.537
ATOM 1490 C8 G X 83 4.252 6.089 -1.327
ATOM 1491 N7 G X 83 3.957 5.376 -0.282
ATOM 1492 C5 G X 83 3.473 4.208 -0.827
ATOM 1493 C6 G X 83 3.005 3.061 -0.159
ATOM 1494 O6 G X 83 2.942 2.890 1.064
ATOM 1495 N1 G X 83 2.590 2.068 -1.054
ATOM 1496 C2 G X 83 2.629 2.186 -2.432
ATOM 1497 N2 G X 83 2.185 1.128 -3.130
ATOM 1498 N3 G X 83 3.069 3.273 -3.071
ATOM 1499 C4 G X 83 3.479 4.245 -2.208
TER
ATOM 1506 N9 CUA M 90 18.599 -19.496 5.363
ATOM 1507 C8 CUA M 90 19.317 -18.826 6.330
ATOM 1508 N7 CUA M 90 19.960 -17.765 5.878
ATOM 1509 C5 CUA M 90 19.606 -17.738 4.549
ATOM 1510 C6 CUA M 90 19.944 -16.854 3.520
ATOM 1511 N6 CUA M 90 20.739 -15.818 3.734
ATOM 1512 N1 CUA M 90 19.447 -17.084 2.287
ATOM 1513 C2 CUA M 90 18.651 -18.139 2.096
ATOM 1514 N3 CUA M 90 18.270 -19.058 2.981
ATOM 1515 C4 CUA M 90 18.784 -18.792 4.203
END
> 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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- application/octet-stream attachment: CUA.mol2
Received on Wed Nov 04 2009 - 18:30:02 PST
