Hi, Mey,
Your procedure has two problems. First of all, the net charge of the residue
is not integral. You may specify the net charge of the residue in the
mainchain .dat file. Secondly, when you generate the topology file with
leap, you forgot to load protein force field parameters. Only loaded
gaff.dat and CRA.frcmod file is not enough since you mixed the AMBER and
gaff atom types in the prepi file.
Best
Junmei
On Thu, Mar 13, 2008 at 9:03 AM, Mey Khalili <ejdehayedosar.gmail.com>
wrote:
>
> 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 - 06:07:49 PDT
