AMBER Archive (2007)

Subject: RE: AMBER: Bad residue/molecule data in prmtop

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jul 25 2007 - 09:17:00 CDT


Dear Neva,

Can you try building the prmtop file again from scratch and see what you
get. Then please post a copy of exactly what you did to create this prmtop
file including the original pdb you used and the commands you gave Leap etc.

Do you get the exact same problem if you run in serial?

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of neva_at_mmb.pcb.ub.es
> Sent: Wednesday, July 25, 2007 06:03
> To: amber_at_scripps.edu
> Subject: AMBER: Bad residue/molecule data in prmtop
>
> Hi all,
>
> I have a problem with a prmtop file,I think. When I run a MD
> of my system
> (double strand DNA with a complex) with amber 8, parallel
> run, I have the
> following message:
>
> | ERROR: Bad residue/molecule data in prmtop!
> | Residue 13(atoms 374- 404) is in
> multiple molecules.
>
> Then I generate a pdb from prmtop and coordinate file with ambpdb,
> but it give me a pdb file with a TER in the middle of the 13°
> residue, instead
> after the 12 residue.
> I carefully double-checked that the sequence and names of
> atom types correspond
> to the standard library. Moreover the complex binding the DNA
> is placed after
> the DNA.
> What I can do? Which is the problem? Can you help me
> please
> Thank you a lot
>
> Neva
>
> --------------------------------------------------------------
> ---------
> 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