AMBER Archive (2009)

Subject: [AMBER] Creating new residue with tleap.

From: rrd (rrd_at_seznam.cz)
Date: Wed Nov 11 2009 - 05:02:23 CST

Hello,

I tried create new residue in tleap, but it didn't work than.
My residue is similar to LEU, but without N atom and without tree H atoms bonded on it.
Instead N atom I put there one H atom (with help of Chimera). So my pdb looks like this :

ATOM 1 CA LEM 1 3.970 2.846 0.000 1.00 0.00 C
ATOM 2 HA LEM 1 3.672 3.400 -0.890 1.00 0.00 H
ATOM 3 CB LEM 1 3.577 3.654 1.232 1.00 0.00 C
ATOM 4 2HB LEM 1 2.497 3.801 1.241 1.00 0.00 H
ATOM 5 3HB LEM 1 3.877 3.116 2.131 1.00 0.00 H
ATOM 6 CG LEM 1 4.274 5.010 1.195 1.00 0.00 C
ATOM 7 HG LEM 1 5.354 4.863 1.186 1.00 0.00 H
ATOM 8 CD1 LEM 1 3.853 5.763 -0.063 1.00 0.00 C
ATOM 9 1HD1 LEM 1 2.773 5.910 -0.055 1.00 0.00 H
ATOM 10 2HD1 LEM 1 4.352 6.732 -0.090 1.00 0.00 H
ATOM 11 3HD1 LEM 1 4.134 5.186 -0.944 1.00 0.00 H
ATOM 12 CD2 LEM 1 3.881 5.818 2.427 1.00 0.00 C
ATOM 13 1HD2 LEM 1 4.182 5.280 3.326 1.00 0.00 H
ATOM 14 2HD2 LEM 1 4.379 6.787 2.400 1.00 0.00 H
ATOM 15 3HD2 LEM 1 2.801 5.965 2.436 1.00 0.00 H
ATOM 16 C LEM 1 5.486 2.705 0.000 1.00 0.00 C
ATOM 17 O LEM 1 6.009 1.593 0.000 1.00 0.00 O
ATOM 18 1HA LEM 1 3.494 1.865 0.018 1.00 0.00 H

1HA is added H atom, and I changed name of residue from LEU to LEM.
Then I started as in tutorial, loaded pdb to tleap:

LEM=loadpdb lprm.pdb
Matching PDB residue names to LEaP variables.
(Residue 0: LEM, Terminal/last, was not found in name map.)
Unknown residue: LEM number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: LEM sequence: 1
Created a new atom named: CA within residue: .R<LEM 1>
Created a new atom named: HA within residue: .R<LEM 1>
Created a new atom named: CB within residue: .R<LEM 1>
Created a new atom named: HB2 within residue: .R<LEM 1>
Created a new atom named: HB3 within residue: .R<LEM 1>
Created a new atom named: CG within residue: .R<LEM 1>
Created a new atom named: HG within residue: .R<LEM 1>
Created a new atom named: CD1 within residue: .R<LEM 1>
Created a new atom named: HD11 within residue: .R<LEM 1>
Created a new atom named: HD12 within residue: .R<LEM 1>
Created a new atom named: HD13 within residue: .R<LEM 1>
Created a new atom named: CD2 within residue: .R<LEM 1>
Created a new atom named: HD21 within residue: .R<LEM 1>
Created a new atom named: HD22 within residue: .R<LEM 1>
Created a new atom named: HD23 within residue: .R<LEM 1>
Created a new atom named: C within residue: .R<LEM 1>
Created a new atom named: O within residue: .R<LEM 1>
Created a new atom named: HA1 within residue: .R<LEM 1>
  total atoms in file: 18
  The file contained 18 atoms not in residue templates

Ok, then I tried define atomtypes (from leaprc.ff99sb):

> addatomtypes {
> { "CA" "C" "sp2" }
> { "HA" "H" "sp3" }
> { "CB" "C" "sp2" }
> { "HB" "H" "sp3" }
> { "CG" "C" "sp2" }
> { "HG" "H" "sp3" }
> { "CD" "C" "sp2" }
> { "HD" "H" "sp3" }
> { "O" "O" "sp2" }
> { "C" "C" "sp2" }
> }

Then set head and tail and charges:
set LEM.1 connect1 LEM.1.C
set LEM.1 connect0 LEM.1.CD1 (this is maybe wrong, I don't know which atom is head, but for now, does't matter)

> set LEM.1.CA charge -0.0902
> set LEM.1.CA charge -0.147200
> set LEM.1.HA charge 0.058500
> set LEM.1.CB charge -0.074400
> set LEM.1.HB2 charge 0.047200
> set LEM.1.HB3 charge 0.060900
> set LEM.1.CG charge -0.075200
> set LEM.1.HG charge 0.056400
> set LEM.1.CD1 charge -0.090200
> set LEM.1.HD11 charge 0.032700
> set LEM.1.HD12 charge 0.038800
> set LEM.1.HD13 charge 0.030100
> set LEM.1.CD2 charge -0.088800
> set LEM.1.HD21 charge 0.035400
> set LEM.1.HD22 charge 0.035800
> set LEM.1.HD23 charge 0.032000
> set LEM.1.C charge 0.657200
> set LEM.1.O charge -0.617700
> set LEM.1.HA1 charge 0.075600

And then, saved it as lib:
saveoff LEM lem.lib

When I then run tleap, and load lem.lib and my pdb file where is sequence of LEM+PRO+ARG, it said :

Mapped residue ARG, term: Terminal/last, seq. number: 2 to: CARG.
One sided connection. Residue: missing connect1 atom.
Joining PRO - CARG

And when I tried save parm, it said:

FATAL: Atom .R<LEM 1>.A<HA1 18> does not have a type.
FATAL: Atom .R<LEM 1>.A<O 17> does not have a type.
FATAL: Atom .R<LEM 1>.A<C 16> does not have a type.
FATAL: Atom .R<LEM 1>.A<HD23 15> does not have a type.
FATAL: Atom .R<LEM 1>.A<HD22 14> does not have a type.
FATAL: Atom .R<LEM 1>.A<HD21 13> does not have a type.
FATAL: Atom .R<LEM 1>.A<CD2 12> does not have a type.
FATAL: Atom .R<LEM 1>.A<HD13 11> does not have a type.
FATAL: Atom .R<LEM 1>.A<HD12 10> does not have a type.
FATAL: Atom .R<LEM 1>.A<HD11 9> does not have a type.
FATAL: Atom .R<LEM 1>.A<CD1 8> does not have a type.
FATAL: Atom .R<LEM 1>.A<HG 7> does not have a type.
FATAL: Atom .R<LEM 1>.A<CG 6> does not have a type.
FATAL: Atom .R<LEM 1>.A<HB3 5> does not have a type.
FATAL: Atom .R<LEM 1>.A<HB2 4> does not have a type.
FATAL: Atom .R<LEM 1>.A<CB 3> does not have a type.
FATAL: Atom .R<LEM 1>.A<HA 2> does not have a type.
FATAL: Atom .R<LEM 1>.A<CA 1> does not have a type.

Why there are these errors? I thought that I defined it before with atomtypes.
Sorry that this is maybe basic question, but I didn't find answer on it. I know that I do something wrong.

Thank you very much for help me with this.

With regards,

Pavel

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