AMBER Archive (2008)

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

From: Mey Khalili (ejdehayedosar_at_gmail.com)
Date: Mon Mar 17 2008 - 08:59:01 CDT

 Hi Junmei

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.

 I don't think that is the problem. When I change the atom nomenclature
from lower case to upper case (following DAP.prepi in the DNA tutorial), I
can connect the residue regardless of the wrong charge. Please see the
attached file, test.prepi, and compare with CRA.prepi. The only difference
between these two is is the atom names. test.prepi works, CRA.prepi doesn't.

> Secondly, when you generate the topology file with leap, you forgot to
> load protein force field parameters. Only loaded gaff.dat and CRA.frcmodfile is not enough since you mixed the AMBER and gaff atom types in the
> prepi file.

  Is this mistake at the level of antechamber or leap? I always load all
the force-field parameters when I start leap (I set it in my shell script).
Here are all the parameters I load. Am I missing something?
Welcome to LEaP!
Sourcing: /usr/local/fbscapp/amber9/dat/leap/cmd/leaprc.ff99
Log file: ./leap.log
Loading parameters: /usr/local/fbscapp/amber9/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02
/04/99
Loading library: /usr/local/fbscapp/amber9/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/fbscapp/amber9/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/fbscapp/amber9/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/fbscapp/amber9/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/fbscapp/amber9/dat/leap/lib/ions94.lib
Loading library: /usr/local/fbscapp/amber9/dat/leap/lib/solvents.lib

  However, I think I might not load the correct force-field parameters for
antechamber. Because instead of generating the upper case atom types like
DAP.prepi, it uses the lower case nomenclature. If this is the problem, how
do I make antechamber use the general force-field and not gaff's? Thanks.

  Best wishes

  Mey

>
>
> On Thu, Mar 13, 2008 at 9:03 AM, Mey Khalili <ejdehayedosar_at_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
> >
> >
> >
> >
> >
> >
>



  • application/octet-stream attachment: CRA.prepi
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