Daniel Wetzler schrieb:
>
> Hallo,
>
> I'm trying to repeat the task of calculating the protein-stability using
> the mm_pbsa.pl skript.
> To perform my task I just copied the configuration file of the
> example and adapted it to my files.
>
> At the first step I created Snapshots of my mdcrd-file using an adapted
> configuration-file.
>
> My problem is now, that the .crd files created by the script do not
> comply to my
> .top (topology-files).
> I can't perform the calculation of the stability because I get the error :
>
> FATAL: NATOM mismatch in coord and topology files
>
> If I want to calculate pdb-files out of my .crd-files I also get an error :
>
> daw.cu16 mmpbsa > ambpdb -p sgdphe_protein.top_alt <
> sgdphe_protein_com.crd.1 > sgdphe_protein_com.pdb.1
> | New format PARM file being parsed.
> | Version = 1.000 Date = 10/25/04 Time = 18:43:24
>
> ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 13613 3907
>
> Does nayone know why my .top files don't comply my .crd-files ?
Probably you stripped water molecules and counter ions when generating
your snapshots (which is the correct way to do). That's why you have
fewer atoms in your snapshots than in the prmtop file you used for the
simulation.Thus, you need to generate a new parmtop file that contains
the protein only and use this in connection with the snapshot files.
Best regards
Holger
>
> Hope anyone can help.
>
> Best wishes,
>
> Daniel
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Nov 05 2004 - 16:53:00 PST
