[gmx-users] RNA compatiable FF in GROMACS3.3

[Maik Goette]

Hi

I suggest to install GROMACS 3.3.
Then load the V3.3-Amber-FF file.
Include it in the FF.dat or place it in the local dir.
Then take the PDB-File and modify it according to the suggestions on the 
authors page.
I also offer to send you my modified amberff-files for 3.3.
I did several modifications concerning:

1. The terminal bases naming (escpecially the terminal OH-Group)
2. Atom names and additional bases (of no interest for you)

If you rename the stuff in your PDB according to the changes, everything 
should run fine.

If you post problems, resulting in an error-output of G-Tools, please 
post the complete error.
I also had several problems in the beginning and mostly it was because 
of mismatches in atom or residue naming.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


raja wrote:
> Dear Mr.Yang Ye and other GMXIONs,
> 
> Thank for your mail...I downloaded AMBER forcefild package from
> folding at HOME site. I unpacked and put amber99 forcefield files inside
> the top folder and tried to run it. Once again it showed simillar error
> in pdb2gmx run. as 
> Fatel error in .rtp file... What I should do now ?
> Please let me what are all the recessary prerequiste to use pdb2gmx for
> a RNA pdb file using AMBER99 force field in
> GROMACS3.3.
> 
> Thanks !
> B.Nataraj
> 
> 
> 
> 
> 
> On Thu, 2 Feb 2006 21:36:13 +0800, "Yang Ye"
> <leafyoung81-group at yahoo.com> said:
> 
>>I recommend you to use amber's gromacs port from folding at home group.
>>
>>I had some personal communication with that Russian group and I was
>>suggested to that as well.
>>
>>Yang Ye
>>
>>-----Original Message-----
>>From: gmx-users-bounces at gromacs.org
>>[mailto:gmx-users-bounces at gromacs.org]
>>On Behalf Of raja
>>Sent: Thursday, February 02, 2006 9:07 PM
>>To: Discussion list for GROMACS users
>>Subject: [gmx-users] RNA compatiable FF in GROMACS3.3
>>
>>Dear GMXIONS,
>>         For RNA simulation , with reference to userforum and
>>         contribution from gromacs webpage, I got force field from
>>         http://rnp-group.genebee.msu.su/3d/oplsa_ff.html. But when I
>>         use it for RNA of my interst ,it shows Fatel error and
>>         referring error in .rtp file. Please help anyone experince in
>>         RNA simulation in GROMACS3.3 in cygwin. 
>>
>>With thanks !
>>B.Nataraj
>>-- 
>>  raja
>>  raja_28 at fastmail.us
>>
>>-- 
>>http://www.fastmail.fm - Does exactly what it says on the tin
>>
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