Dear Alex,
- You _MUST_ check the impact of this intra-mcc on the fitting step in
your case! We hope to extend the application of the statistics module
in this case...
- Rounding off errors at 10-4 (or 10-3/10-2) is another issue; I hope
we will release soon an answer to this problem for a large collection
of FF libs in relation with the "addions" command of LEaP. Check that
the total charge of your unit exactly equals to what you expect...
- Now, the answer related to your question: the "sequence" command is
convenient to build test models (i.e. test bond connection between
units), but in general it is not used to generate an input set of
Cartesian coordinates for MD simulations (except if you do not have
any experimental structure). So in general, you load all the FF
libraries in LEaP, and then the PDB file (i.e. experimental data with
the set of 'wanted' Cartesian coordinates) of your polymer with your
RNA-peptide modification;
-> the FF libs will match the PDB file if the residue/atom names in
the PDB file agree withe these in the FF libs, and you will generate
the prmtop/prmcrd files for your molecular system with the 'wanted'
Cartesian coordinates...
I hope this helps...
regards, Francois
> i need a little explanation in tleap usage. In the begining of my work
> I had a 3d structure of RC5-RC-RA-NVA (ligand). I used a lot of
> advices from q4md-fft.q4md-forcefieldtools.org and after preparations
> in REDIII I started to create a topology fo amber and gromacs... Mol2
> files for nucleics I createds with tleap from pdb files, their
> coordinates were identical.
> ThenI used tleap and this commands to obtain topology files:
>
> tleap -s -f leaprc.ff99SB
>
> RC5 = loadmol2 rc5.mol2
> set RC5 name "RC5"
> set RC5 tail RC5.1.O3'
> set RC5.1 connect0 RC5.1.H5T
> set RC5.1 connect1 RC5.1.O3'
> set RC5.1 restype nucleic
> set RC5.1 name "RC5"
>
> .....
>
> NVA = loadmol2 nvach_red.mol2
> set NVA name "NVA"
> set NVA head NVA.1.C
> set NVA.1 connect0 NVA.1.C
> set NVA.1 restype protein
> set NVA.1 name "NVA"
>
> RRRN = sequence { RC5 RC RA NVA }
>
> savemol2 RRRN rrrn.mol2 1
> saveamberparm RRRN rrrn.prmtop rrrn.prmcrd
>
> And when I looked at rrrn.mol2 model in the viewer I saw that its
> coordinates are absoluetly different from the initial structure!
>
> The question is: whether this moment is important for topology
> creation or not? If it is, so how to avoid this problem?
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Received on Wed Feb 01 2012 - 09:30:02 PST
