As Elaine said, use Help..Report a Bug in the Chimera menu, not as the subject line of another mail! Anyway, the info you provided below is enough for me to diagnose the problem. In 1SVC, the proline at position 43 in chain P is missing its main chain nitrogen. You either need to add the nitrogen back (with the Build Structure tool) or delete that residue. Deleting the residue is simplest. To do that, open the command line (Favorites->Command Line) and type: del :43.p You should then be able to minimize the structure without error. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Nov 26, 2012, at 9:41 PM, amna khan wrote:
hi, when i minimize my structure it gives the following error for my pdb file. that prolone residues is missing and about integral charges.
please help me to remove this error
#0, chain D: dna (5'- D(*ap*gp*ap*tp*gp*gp*gp*gp*ap*ap*tp*cp*cp*cp*cp*tp*A P*gp*A)-3')
#0, chain P: nuclear factor
κ-B (nf-kb)
Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records
Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records
Chain-initial residues that are actual N terminii: DA 1.D
Chain-initial residues that are not actual N terminii: PRO 43.P
Chain-final residues that are actual C terminii: DA 19.D
Chain-final residues that are not actual C terminii: GLU 353.P
321 hydrogen bonds
Removing spurious proton from 'C' of GLU 353.P
Hydrogens added
No incomplete side chains
Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records
Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records
Chain-initial residues that are actual N terminii: DA 1.D
Chain-initial residues that are not actual N terminii: PRO 43.P
Chain-final residues that are actual C terminii: DA 19.D
Chain-final residues that are not actual C terminii: GLU 353.P
188 hydrogen bonds
Removing spurious proton from 'C' of GLU 353.P
Hydrogens added
Charge model: AMBER ff99SB
Total charge for #0: -15.624
The following residues had non-integral charges:
DA 1.D -0.3079
DA 19.D -0.6921
PRO 43.P 0.376
1 model(s) had non-integral total charge
Details in reply log
Residue #0:43.P (PRO/proline) is missing atoms H_3 and H_2
No incomplete side chains
Terminii for 1SVC.pdb (#0) chain D determined from SEQRES records
Terminii for 1SVC.pdb (#0) chain P determined from SEQRES records
Chain-initial residues that are actual N terminii: DA 1.D
Chain-initial residues that are not actual N terminii: PRO 43.P
Chain-final residues that are actual C terminii: DA 19.D
Chain-final residues that are not actual C terminii: GLU 353.P
188 hydrogen bonds
Removing spurious proton from 'C' of GLU 353.P
Hydrogens added
Charge model: AMBER ff99SB
Total charge for #0: -15.624
The following residues had non-integral charges:
DA 1.D -0.3079
DA 19.D -0.6921
PRO 43.P 0.376
1 model(s) had non-integral total charge
Details in reply log
Residue #0:43.P (PRO/proline) is missing atoms H_2 and H_3
regards
amna khan
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