AMBER Archive (2009)

Subject: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Nov 04 2009 - 23:42:43 CST

Dear Zhou Gong,

> Have you just modified the TER line in the PDB file ? I have
> done this like your addivise, like

& shifted the atom number column: added three space characters - only for CUA

> 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 ?

Yes I got this second/new problem as well.

Did you remove the hydrogens of CUA on purpose ?

You need to define the FF atom type & see how it goes:
See the addAtomTypes command in LEaP & see leaprc.ff99SB to see how to
use this command.

regards, Francois

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