AMBER Archive (2005)

Subject: AMBER: A question on connecting residues in xleap

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Sun Apr 10 2005 - 11:54:55 CDT

Dear amber-users,

I'm trying to make prmtop and inpcrd of a molecule and have some problems in
xleap.
COR residue is N-CH2-CH2-N, and I want to attach 4 DEN residues to COR residue
(two DEN residues per each N of COR residues). However, since the sequence
numbers of the residues are determined from the order of residues in the PDB
file, xleap tried to make COR-DEN-DEN-DEN instead of making
DEN-COR-DEN
 DEN/ \DEN, and then finally show errors saying that there is huge distance
between bonded atoms, which are not supposed to be bonded.
Could you tell me how to fix this problem and attach DEN residues to N atoms of
COR?? (attaching same type of residues to the core molecule symmetrically)
This is huge molecule (dendrimer), and I'll have to repeat to attach same
resiudes like this.
Leap log file and my pdb file are shown below.

---------------------------
> model = loadpdb "test0.pdb"
Loading PDB file: ./test0.pdb
Matching PDB residue names to LEaP variables.
(Residue 0: COR, Terminal/beginning, was not found in name map.)
(Residue 1: DEN, Nonterminal, was not found in name map.)
(Residue 2: DEN, Nonterminal, was not found in name map.)
(Residue 3: DEN, Nonterminal, was not found in name map.)
(Residue 4: DEN, Terminal/last, was not found in name map.)
Joining COR - DEN
Joining DEN - DEN
Joining DEN - DEN
Joining DEN - DEN
  total atoms in file: 76
> saveamberparm model test0.prmtop test0.inpcrd
Checking Unit.
WARNING: There is a bond of 5.327936 angstroms between:
------- .R<COR 1>.A<N 8> and .R<DEN 2>.A<C1 1>
WARNING: There is a bond of 10.503986 angstroms between:
------- .R<DEN 2>.A<N 17> and .R<DEN 3>.A<C1 1>
WARNING: There is a bond of 14.061881 angstroms between:
------- .R<DEN 3>.A<N 17> and .R<DEN 4>.A<C1 1>
WARNING: There is a bond of 10.497902 angstroms between:
------- .R<DEN 4>.A<N 17> and .R<DEN 5>.A<C1 1>

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: c3 - n1 - c3
Building proper torsion parameters.
Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for c3-o-c2-n
        atoms are: C2 O2 C N1
 ** Warning: No sp2 improper torsion term for c3-o-c2-n
        atoms are: C2 O2 C N1
 ** Warning: No sp2 improper torsion term for c3-o-c2-n
        atoms are: C2 O2 C N1
 ** Warning: No sp2 improper torsion term for c3-o-c2-n
        atoms are: C2 O2 C N1
old PREP-specified impropers:
 <DEN 2>: C2 N1 C O2
 <DEN 3>: C2 N1 C O2
 <DEN 4>: C2 N1 C O2
 <DEN 5>: C2 N1 C O2
 total 4 improper torsions applied
 4 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.
--------------------------------
HEADER GROwing Monsters And Cloning Shrimps
MODEL 1
ATOM 1 C1 COR 1 -0.475 4.304 -2.189 1.00 0.00
ATOM 2 C2 COR 1 1.190 4.219 -2.059 1.00 0.00
ATOM 3 N1 COR 1 2.334 5.334 -1.690 1.00 0.00
ATOM 4 N COR 1 -1.633 3.162 -2.399 1.00 0.00
ATOM 5 H11 COR 1 -0.647 5.067 -2.972 1.00 0.00
.
.
ATOM 9 C1 DEN 2 2.443 6.582 -2.676 1.00 0.00
ATOM 10 C2 DEN 2 3.111 8.054 -2.373 1.00 0.00
ATOM 11 C DEN 2 3.447 9.227 -3.495 1.00 0.00
ATOM 12 O2 DEN 2 3.531 8.862 -4.663 1.00 0.00
ATOM 13 N1 DEN 2 3.704 10.604 -3.243 1.00 0.00
ATOM 14 C3 DEN 2 4.230 11.665 -4.292 1.00 0.00
ATOM 15 C4 DEN 2 4.175 13.300 -4.076 1.00 0.00
ATOM 16 N DEN 2 4.938 14.503 -4.841 1.00 0.00
.
.
ATOM 26 C1 DEN 3 3.749 4.682 -1.310 1.00 0.00
ATOM 27 C2 DEN 3 4.588 4.768 0.098 1.00 0.00
ATOM 28 C DEN 3 5.979 3.927 0.430 1.00 0.00
ATOM 29 O2 DEN 3 6.308 3.066 -0.381 1.00 0.00
ATOM 30 N1 DEN 3 6.823 4.080 1.565 1.00 0.00
ATOM 31 C3 DEN 3 8.065 3.174 1.935 1.00 0.00
ATOM 32 C4 DEN 3 9.174 3.546 3.100 1.00 0.00
ATOM 33 N DEN 3 10.330 2.658 3.800 1.00 0.00
.
.
ATOM 43 C1 DEN 4 -1.536 2.300 -3.737 1.00 0.00
ATOM 44 C2 DEN 4 -2.204 0.829 -4.038 1.00 0.00
ATOM 45 C DEN 4 -2.313 0.088 -5.517 1.00 0.00
ATOM 46 O2 DEN 4 -2.212 0.811 -6.502 1.00 0.00
ATOM 47 N1 DEN 4 -2.569 -1.289 -5.767 1.00 0.00
ATOM 48 C3 DEN 4 -2.883 -1.943 -7.173 1.00 0.00
ATOM 49 C4 DEN 4 -2.817 -3.561 -7.487 1.00 0.00
ATOM 50 N DEN 4 -3.408 -4.434 -8.713 1.00 0.00
.
.
ATOM 60 C1 DEN 5 -3.110 3.695 -2.077 1.00 0.00
ATOM 61 C2 DEN 5 -4.173 3.185 -0.935 1.00 0.00
ATOM 62 C DEN 5 -5.628 3.908 -0.599 1.00 0.00
ATOM 63 O2 DEN 5 -5.849 4.982 -1.147 1.00 0.00
ATOM 64 N1 DEN 5 -6.643 3.424 0.274 1.00 0.00
ATOM 65 C3 DEN 5 -7.964 4.192 0.686 1.00 0.00
ATOM 66 C4 DEN 5 -9.233 3.499 1.481 1.00 0.00
ATOM 67 N DEN 5 -10.524 4.148 2.208 1.00 0.00
.
.
TER

best,
Hwankyu.
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