AMBER Archive (2009)

Subject: [AMBER] Error in minimal

From: xuemeiwang1103 (xuemeiwang1103_at_163.com)
Date: Tue Sep 15 2009 - 02:27:18 CDT

Dear Amber users:
    Thaks for anwsering my questions.
    At this moment I have to ask another question.Now, I have done minimisation ,but there is some wrong ,tne min1.in is:
  &cntrl
  imin=1,
  maxcyc=5000
  ncyc=1000,
  cut=999, rgbmax=999,
  ntb=0,
  igb=1,
  ntpr=100
/
The out is:
error:
ifbox=2 in prmtop but angles are not correct
I want to kown the mean of the error.By the way ,my pdb files are short of some residues which is download from the RSCB,so I can't save the top and crd files .In order to solve the problem I add the TER between Ser434 and Ser439 ,then I solve the complex in TIP3PBOX 12 ,everything seems ok until I run the Minmal.Could someone tell me if it is wrong what I did with my pdb and the reason about the error above,Ithank you£¡
 my original pdb :
......
ATOM 3193 CB SER A 434 65.500 21.805 30.926 1.00 44.95 C
ATOM 3194 OG SER A 434 64.454 21.428 30.048 1.00 47.16 O
ATOM 3195 N SER A 439 64.492 32.666 21.953 1.00 45.58 N
ATOM 3196 CA SER A 439 63.932 31.868 20.878 1.00 45.90 C
......
 

 

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber