Thanks to Eric Pettersen I have fixed problems of long bonds and mis-assignement by prepare_amber.pl (from HIS to HIE, while it is HID). Two types of problems remain because I was either unable to correct or did wrongly. The error log from attempted fixing problems: WARNING: The unperturbed charge of the unit: 24.000000 is not zero. FATAL: Atom .R<GLH 443>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 402>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 386>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 375>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 373>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 334>.A<H 14> does not have a type. FATAL: Atom .R<GLH 332>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 291>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 275>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 264>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 262>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 223>.A<H 14> does not have a type. FATAL: Atom .R<GLH 221>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 180>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 164>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 153>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 151>.A<HE1 17> does not have a type. FATAL: Atom .R<GLH 128>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 112>.A<H 14> does not have a type. FATAL: Atom .R<GLH 110>.A<HE1 17> does not have a type. FATAL: Atom .R<ASH 69>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 53>.A<HD1 14> does not have a type. FATAL: Atom .R<ASH 42>.A<HD1 14> does not have a type. FATAL: Atom .R<GLH 40>.A<HE1 17> does not have a type. FATAL: Atom .R<GLH 17>.A<HE1 17> does not have a type. FATAL: Atom .R<NSER 1>.A<H 14> does not have a type. UNABLE : I don't know how to rename the hydrogen on serine nitrogen. In my protein.pdb, the section around residues 333/334: ATOM 5155 O THR X 333 15.694 -15.150 25.132 0.00 0.00 O TER 5156 THR X 333 ATOM 5157 N SER X 334 -16.176 22.312 10.940 0.00 0.00 N ATOM 5158 H SER X 334 -15.301 22.760 10.966 0.00 0.00 H ATOM 5159 CA SER X 334 -16.224 20.932 11.429 0.00 0.00 C ATOM 5160 HA SER X 334 -17.198 20.770 11.905 0.00 0.00 H ATOM 5161 CB SER X 334 -15.868 19.959 10.306 0.00 0.00 C ATOM 5162 HB2 SER X 334 -15.761 18.918 10.709 0.00 0.00 H ATOM 5163 HB3 SER X 334 -14.903 20.280 9.956 0.00 0.00 H ATOM 5164 OG SER X 334 -16.906 19.973 9.300 0.00 0.00 O ATOM 5165 HG SER X 334 -16.948 20.844 8.983 0.00 0.00 H ATOM 5166 C SER X 334 -15.185 20.856 12.533 0.00 0.00 C ATOM 5167 O SER X 334 -14.212 21.643 12.566 0.00 0.00 O Actually, I only inserted "TER" (where it is now) between residue 333 and 334 to get rid of a long bond between the two; numbering and THR X 333 came out automatically. Also, automatically the pdb file now begins with a series of HELIX. BADLY DONE: to correct for the carboxyl hydrogen being on the wrong oxygen of ASP (renamed ASH) and GLU (renamed GLH), for example, for 443 the section ATOM 6851 CD GLU X 443 -10.347 20.009 21.724 0.00 0.00 ATOM 6852 OE1 GLU X 443 -10.341 20.227 23.079 0.00 0.00 ATOM 6853 OE2 GLU X 443 -10.192 20.919 20.907 0.00 0.00 ATOM 6854 HE1 GLU X 443 -10.239 21.145 23.232 0.00 0.00 was rewritten by exchanging two lines, which automatically were renumbered ATOM 6854 CD GLH X 443 -10.347 20.009 21.724 0.00 0.00 C ATOM 6855 OE1 GLH X 443 -10.341 20.227 23.079 0.00 0.00 O ATOM 6856 OE2 GLH X 443 -10.192 20.919 20.907 0.00 0.00 O ATOM 6857 HE1 GLH X 443 -10.239 21.145 23.232 0.00 0.00 H ATOM 6858 C GLH X 443 -13.205 16.911 22.895 0.00 0.00 C and the issue on prepare_amber.pl was not resolved. It is obvious that I am carrying out such adjustments for the first time. I got the impression that from now on, what I do increases the mess. Must say that with my imperfect pdb I could carry outt all DOCK tutorials, except the amber_score. Thanks francesco pietra __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com