AMBER Archive (2008)

Subject: Re: AMBER: LEap error message for parmBSC0 force field

From: Alberto Perez (raist_at_mmb.pcb.ub.es)
Date: Thu Apr 03 2008 - 09:00:09 CDT

Hi Cenk,
I was trying to reproduce what you were doing, and you are right about the
improper messages, but it is not an error, they are just warnings and your
topology and coordinate files should be saved without any problem.
If you do the same process without loading the parmbsc0 forcefield and
libraries and with a verbosity of 2 you will see some warning about
improper dihedrals (except those involving atom type CI).
The only thing that I would change in the parmbsc0 library is the
perturbed atom type for atom name C5' which should be CI and is CT,
but you don't have to worry about it if you are not using a perturbed
topology file.
Hope it helps.
Alberto

----------------------------------------------------------------
Alberto Perez
Molecular Modeling & Bioinformatics group

IRBB Parc Cientific de Barcelona | e-mail:raist_at_mmb.pcb.ub.es
Universitat de Barcelona | phone: + 34 93 403 71 55
Josep Samitier,1-5 | FAX: + 34 93 403 71 57
08028 Barcelona (Spain) | phone BSC: +34 93 413 76 02

On Thu, 3 Apr 2008, Cenk Andac wrote:

> Hi Tom,
>
> Thank you for responding.
>
> here is how I loaded the force field libraries and parameters in LEap.
>
>> source leaprc.rna.ff99
> Sourcing: /usr/local/amber9/dat/leap/cmd/leaprc.rna.ff99
> Log file: ./leap.log
> Loading parameters: /usr/local/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/amber9/dat/leap/lib/all_nucleic94.lib
> Loading library: /usr/local/amber9/dat/leap/lib/all_amino94.lib
> Loading library: /usr/local/amber9/dat/leap/lib/all_aminoct94.lib
> Loading library: /usr/local/amber9/dat/leap/lib/all_aminont94.lib
> Loading library: /usr/local/amber9/dat/leap/lib/ions94.lib
> Loading library: /usr/local/amber9/dat/leap/lib/solvents.lib
>> parmbsc0=loadamberparams parmbsc0.params
> Loading parameters: ./parmbsc0.params
> Reading force field modification type file (frcmod)
> Reading title:
> torsion chi y gamma
>> loadoff all_nucleic.parmbsc0.lib
> Loading library: ./all_nucleic.parmbsc0.lib
>
> the improper torsion error messages pop-up with ' verbosity 2 ' only. However,
> there appears that the missing improper torsions are already added eventually by LEap.
> ....
> ....
> ...
> ...
> ** Warning: No sp2 improper torsion term for OS-H1-CI-CT
> atoms are: O5' H5'2 C5' C4'
> ** Warning: No sp2 improper torsion term for H1-H1-CI-CT
> atoms are: H5'1 H5'2 C5' C4'
> --Impropers:
> 1 C1'<RA5> - C8<RA5> - N9<RA5> - C4<RA5>
> 1 C1'<RU3> - C6<RU3> - N1<RU3> - C2<RU3>
> 1 C4<RU3> - H3<RU3> - N3<RU3> - C2<RU3>
> 1 C5<RA5> - N6<RA5> - C6<RA5> - N1<RA5>
> 1 C5<RU3> - O4<RU3> - C4<RU3> - N3<RU3>
> 1 C6<RA5> - H61<RA5> - N6<RA5> - H62<RA5>
> 1 C6<RU3> - H5<RU3> - C5<RU3> - C4<RU3>
> 1 N1<RA5> - H2<RA5> - C2<RA5> - N3<RA5>
> 1 N1<RU3> - H6<RU3> - C6<RU3> - C5<RU3>
> 1 N1<RU3> - N3<RU3> - C2<RU3> - O2<RU3>
> 1 N9<RA5> - H8<RA5> - C8<RA5> - N7<RA5>
> total 11 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (no restraints)
>
> Thomas Cheatham III <tec3_at_utah.edu> wrote:
>> I keep getting the following error message
>> when I try to save a topology file for a 2nt RNA molecule
>> using the new parmBSC0 force field. Could someone please
>> clarify if I am missing something with the installation of the
>> parmBSC0 force field?
>>
>>> verbosity 2
>>> x=sequence {RA5 RG3}
>> Sequence: RA5
>> Sequence: RG3
>> Joining RA5 - RG3
>>> edit x
>>> saveamberparm x a.prmtop a.x
>
> ...without seeing what you are loading (in terms of the leaprc and what
> residue/topology, library, or parameter files) it is tricky to determine,
> but my guess is that you didn't load-up all the necessary library/force
> field files as it is complaining about impropers...
>
> I would try:
>
> tleap -f $AMBERHOME/dat/leap/cmd/leaprc.rna.ff99
> bsc0 = loadamberparams frcmod.parmbsc0
>
> followed by the rest of your script.
>
> -- tec3
>
> regards,
>
> jenk
>
>
> ---------------------------------
> You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost.
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