AMBER Archive (2003)

Subject: Re: bond command

From: Craig A Bayse (CBayse_at_odu.edu)
Date: Wed Feb 12 2003 - 15:36:29 CST

understood.

basically, i want to model cisplatin-dna complexes. i've modified the
various dat/leap/* files and the parameters load without error. for the
current problem, i load the pdb file and do the following:

bond cab.19.1 cab.5.16
bond cab.19.1 cab.6.16

saveamberparm cab cab.prmtop cab.inpcrd

the error after 'Building proper torsion parameters'
!FATAL ERROR-------------------------------------------------
!FATAL: In file [unitio.c], ;line 1765
!FATAL: Message 1-4: cannot add bond 136 568

                                                                                                     
                      "David A. Case"
                      <case_at_scripps.edu To: Craig A Bayse <CBayse_at_odu.edu>
> cc: amber_at_heimdal.compchem.ucsf.edu
                                               Subject: Re: bond command
                      02/06/03 01:13 AM
                      Please respond to
                      amber
                                                                                                     
                                                                                                     

On Wed, Feb 05, 2003, Craig A Bayse wrote:
>
> I figured out the problem, but when i try to save the prmtop and inpcrd
> files, i get an error that says i cannot add the bond.

Can you give more details: what commands did you give to LEaP? What was
the *exact* error message?

You are telling us what you *tried* to do (save the prmtop and incprd), and
your interpretation of the error message (that you cannot add the bond).

As the lawyers say, this is not the "best evidence". To be effective in
helping you, we need to know what you actually did (the commands you typed)
and what the computer actually said (the error message).

[A note: the above comments are directed not just at you, but at other
participants in the amber mailing list as well: please try double-hard
to be as expicit as you can in reporting problems!]

..thanks!...dave case 

--

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================