AMBER Archive (2004)

Subject: Re: AMBER: Is it a bug?(in prep file opls_unict.in)

From: Wu Lei (wulei_at_biophy.nju.edu.cn)
Date: Sat Jul 17 2004 - 00:15:16 CDT

Hi~ dac

look at the last three atoms

     PHENYLALANINE, ALL ATOM AROMATIC PARAMETERS, COO- ANION
 PHE
 PHE INT 1
CORR OMIT DU BEG
  0.00
   1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
   2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
   3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
   4 N N M 3 2 1 1.335 116.600 180.000 -0.57000
   5 HN H E 4 3 2 1.010 119.800 0.000 0.37000
   6 CA CH M 4 3 2 1.449 121.900 180.000 0.10000
   7 CB C2 S 6 4 3 1.525 111.100 60.000 0.11500
   8 CG CK S 7 6 4 1.510 115.000 180.000 -0.11500
   9 CD1 CK B 8 7 6 1.400 120.000 180.000 -0.11500
  10 HD1 HK E 9 8 7 1.090 120.000 0.000 0.11500
  11 CE1 CK B 9 8 7 1.400 120.000 180.000 -0.11500
  12 HE1 HK E 11 9 8 1.090 120.000 180.000 0.11500
  13 CZ CK B 11 9 8 1.400 120.000 0.000 -0.11500
  14 HZ HK E 13 11 9 1.090 120.000 180.000 0.11500
  15 CE2 CK B 13 11 9 1.400 120.000 0.000 -0.11500
  16 HE2 HK E 15 13 11 1.090 120.000 180.000 0.11500
  17 CD2 CK S 15 13 11 1.400 120.000 0.000 -0.11500
  18 HD2 HK E 17 15 13 1.090 120.000 180.000 0.11500
  14 (19?) C C M 6 4 3 1.522 111.100 180.000 0.70000
  15 (20?) O O2 E 14 6 4 1.229 120.500 0.000 -0.80000
  16 (21?) OXT O2 E 14 6 4 1.229 120.500 180.000 -0.80000

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Saturday, July 17, 2004 12:27 AM
Subject: Re: AMBER: Is it a bug?(in prep file opls_unict.in)

> On Fri, Jul 16, 2004, Wu Lei wrote:
>
> > I've found out that the atom sequence number for PHE in file "opls_unict.in"
> > is strange that they are disordered.
>
> What you posted looks fine to me. What do you mean by "strange" and
> "disordered"? Do you have a problem using these files?
>
> ...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu