AMBER Archive (2008)

Subject: AMBER: can't make antechamber work for regular nucleotides

From: Mey Khalili (ejdehayedosar_at_gmail.com)
Date: Thu Mar 13 2008 - 09:03:45 CDT

 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


  • application/zip attachment: all.zip
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