AMBER Archive (2006)

Subject: AMBER: problem loading forcefield leaprc.ff86

From: Mahalakshmi Sahasranaman (mlakshmis_at_gmail.com)
Date: Fri May 19 2006 - 09:27:38 CDT

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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