Hi All,
I am trying to change proline into alanine in a peptide by TI softcore
potential algo. But I am getting Atom coordinate disagreement error. I am
masking
mask0=':PRO.CD,HD2,HD3,CG,HG2,HG3'
mask1=':ALA.HB1,H'
mdin_min_v0
ifsc=1,
crgmask='${mask0}',
scmask='${mask0}',
mdin_min_v1
ifsc=1,
crgmask='${mask1}',
scmask='${mask1}',
getting this error:
Softcore Mask :PRO.CD,HD2,HD3,CG,HG2,HG3; matches 6 atoms
this run corresponds to V0, its softcore atoms interact fully for
lambda=0
this process: 44657 atoms, partner process: 44653 atoms
Checking for mismatched coordinates.
WARNING: Local coordinate 139 differs from partner coordinate 124 !
SANDER BOMB in subroutine sc_check_and_adjust
Atom coordinate disagreement
Check input files.
Please let me know your suggestion to solve this issue.
Thanks
--
-------------------------
Sonu Kumar
Postdoctoral Associate
Infectious and Inflammatory Disease Center
Bioinformatics and System Biology
Sanford-Burnham Medical Research Institute
10901 North Torrey pines Rd
La Jolla, CA 92037
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Received on Thu May 23 2013 - 11:00:04 PDT
