Hello
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?
Thank you
--
Nemo me impune lacessit
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Received on Wed Feb 01 2012 - 03:00:02 PST
