[Chimera-users] Help... Report a Bug

[amna khan]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20121127/596514ce/attachment.html>