Dear AMber users,
I am using amber8 and I am trying to load my dna using leaprc.ff86. I have
introduced a TER card
between residue 10 and residue 11 as indicated in the amber tutorial.
When I load leaprc.ff86 using xleap for vacuum simulations, it says
> adna1 = loadpdb "a-dna.pdb"
Loading PDB file: ./a-dna.pdb
Unknown residue : C5 number :0 type : Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue : C3 number:9 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue : G5 number :10 type : Terminal/Beginning
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue : G3 number:19 type : Terminal/Last
..relaxing end constraints to try for a dbase match
-no luck
At the end, it says
total atoms in file : 446
Leap added 184 missing atoms according to residue templates :
92 Heavy
88 H/ lone pairs
4 Unknown element
The file contained 446 atoms not in residue templates
How do I correct this ? It doesnt seem to identify the residue and says 4
unknown element.
Thanks,
Lakshmi
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Received on Sun May 21 2006 - 06:07:12 PDT
