Dear amber,
I had considerable difficulty finding parameters for a modified RNA
Adenine nucleotide when it comes to connectivity. I decided to test
antechamber on a regular RA. I am using AMBER9.
1-In xleap:
savepdb RA RA.pdb
2-antechamber -fi pdb -fo ac -i RA.pdb -o CRA.ac
(at this stage, I am not concerned with charges, I just want to get the
connectivity right).
3-I change the name to CRA in CRA.ac.
4- I take the connectivity info from here (mainchain.dna), and I change the
nomenclature to fit my atom names.
http://amber.scripps.edu/antechamber/dna.html
5-I make the prepi file:
prepgen -i CRA.ac -o CRA.prepi -f prepi -m mainchain.dna -rn CRA -rf ""
HEAD_ATOM 1 P
TAIL_ATOM 33 O3*
MAIN_CHAIN 1 1 P
MAIN_CHAIN 2 4 O5*
MAIN_CHAIN 3 5 C5*
MAIN_CHAIN 4 8 C4*
MAIN_CHAIN 5 27 C3*
MAIN_CHAIN 6 33 O3*
6-I generate the parameter files:
parmchk -fi prepi -i CRA.prepi -o CRA.frcmd
7-In leap
source leaprc.gaff
8-loadamberprep CRA.prepi
9-loadamberparams CRA.frcmd
10-check CRA (it tells me it is OK).
11-desc CRA tells me head and tail is correct.
11-aa=sequence{RA5 CRA}
12- saveamberparm aa test.prmtop test.inpcrd
I get a bunch of errors:
Checking Unit.
ERROR: The unperturbed charge of the unit: -0.308100 is not integral.
WARNING: The unperturbed charge of the unit: -0.308100 is not zero.
-- ignoring the error and warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: OS - p4
Building angle parameters.
Could not find angle parameter: OS - p4 - o
Could not find angle parameter: OS - p4 - o
Could not find angle parameter: OS - p4 - os
Could not find angle parameter: CT - OS - p4
Building proper torsion parameters.
** No torsion terms for CT-OS-p4-o
** No torsion terms for CT-OS-p4-o
** No torsion terms for CT-OS-p4-os
Building improper torsion parameters.
old PREP-specified impropers:
<CRA 2>: C1* C4 N9 C8
<CRA 2>: H8 N9 C8 N7
<CRA 2>: C6 C4 C5 N7
<CRA 2>: C5 N1 C6 N6
<CRA 2>: C6 H61 N6 H62
<CRA 2>: H2 N1 C2 N3
<CRA 2>: C5 N9 C4 N3
total 12 improper torsions applied
7 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.
I think it has problem connecting RA5 OT to CRA p4. When I look at the DNA
tutorial mentioned above, I notice that atom nomenclature is different. If
this is the problem, how do I switch to atom names in the DNA tutorial.
Attached, please find the zip of all the files I generated along the way
and leap's log file.
Best wishes
Mey
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Received on Sun Mar 16 2008 - 06:07:22 PDT
