AMBER Archive (2008)

Subject: Re: AMBER: saveamberparm error

From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Thu Oct 09 2008 - 05:22:45 CDT

Hi Shaikh,

   Which program were you using, sleap or tleap?

   besides can you send your PDB files and input files?

   Sincerely,

   Wei

On Wed, Oct 8, 2008 at 9:24 PM, Shaikh Abdul R S Ramaju <smasarsr_at_nus.edu.sg
> wrote:

> Dear Dr. Ross,
>
>
>
> While preparing the Cytochrome P450, first I added the missing residues
> using swiss pdb viewer. The I added hydrogen to HEM and cysteine group,
> which is also attached to heme (I didn't added the hydrogen to protein, as
> leap does not recognize it). Then I took the parameters from amber
> contributed parameters (amber9/dat/contrib). As parameters are for
> heme-histidine, I modified it for heme-cysteine. After that I used usual
> procedure using tleap.
>
> Set of commands are as follows-
>
> source leaprc.ff99
>
> loadamberparams parm99_mod.dat
>
> loadamberparams frcmod.heme_all
>
> loadamberprep heme_all.in
>
> mol=loadpdb 2H7S_mod.pdb
>
> check mol
>
>
>
> After check mol I got error message that FE is bonded to backbone C of
> cysteine. According to one of the Amber users suggestion, I deleted that
> bond using deletebond command. Then I didn't find the error about bond
> between FE and C. Finally I tried to save topology file using saveamberparm.
> After "Marking per-residue atom chain types." System get hang at this
> point. No error message is found after this sentence. In my previous message
> I have attached the pdb files and parameter files (
> http://archive.ambermd.org/200810/0053.html). Please find the attached
> file for commands and error message.
>
>
>
> Thanking you
>
> Regards
>
> Abdul Rajjak
>
>
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Ross Walker
> *Sent:* Wednesday, October 08, 2008 11:23 PM
> *To:* amber_at_scripps.edu
> *Subject:* RE: AMBER: saveamberparm error
>
>
>
> Dear Shaikh,
>
>
>
> I don't see any error message in your output below. What exactly do you
> mean by the "System gets stuck"? Does it just hang at this point?
>
>
>
> Can you send us your full set of leap commands, I.e. what you did before
> the saveamberparm, as well as a more in-depth discussion of the pdb you
> used, how you modified it, what parameters you are using etc. and then we
> might be able to work out what is going on.
>
>
>
> All the best
>
> Ross
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Shaikh Abdul R S Ramaju
> *Sent:* Wednesday, October 08, 2008 4:34 AM
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: saveamberparm error
>
>
>
> Dear Amber Users,
>
>
>
> I am trying to prepare amber input files for Cytochrome P450.
>
> When I tried to save to topology file and coordinate file, following
> message appears. After "Marking per-residue atom chain types." System gets
> stuck. It didn't create any topology file. What will be the possible reason
> for this error. I will be grateful for your suggestion.
>
>
>
> Thanks
>
> Abdul Rajjak
>
>
>
> > saveamberparm mol parmtop parmcrd
>
> Checking Unit.
>
> WARNING: The unperturbed charge of the unit: -20.000000 is not zero.
>
>
>
> -- ignoring the warning.
>
>
>
> Building topology.
>
> Building atom parameters.
>
> Building bond parameters.
>
> Building angle parameters.
>
> Building proper torsion parameters.
>
> Building improper torsion parameters.
>
> old PREP-specified impropers:
>
> <HEM 357>: -M CA N H
>
> <HEM 357>: CA +M C O
>
> <HEM 357>: NA C1A C4A FE
>
> <HEM 357>: NB C1B C4B FE
>
> <HEM 357>: NC C1C C4C FE
>
> <HEM 357>: ND C1D C4D FE
>
> <HEM 357>: C1A C2A NA CHA
>
> <HEM 357>: C1B C2B NB CHB
>
> <HEM 357>: C1C C2C NC CHC
>
> <HEM 357>: C1D C2D ND CHD
>
> <HEM 357>: C2A C3A C1A CAA
>
> <HEM 357>: C2B C3B C1B CMB
>
> <HEM 357>: C2C C3C C1C CMC
>
> <HEM 357>: C2D C3D C1D CMD
>
> <HEM 357>: C3A C4A C2A CMA
>
> <HEM 357>: C3B C4B C2B CAB
>
> <HEM 357>: C3C C4C C2C CAC
>
> <HEM 357>: C3D C4D C2D CAD
>
> <HEM 357>: C4A NA C3A CHB
>
> <HEM 357>: C4B NB C3B CHC
>
> <HEM 357>: C4C NC C3C CHD
>
> <HEM 357>: C4D ND C3D CHA
>
> <HEM 357>: C4D C1A CHA HGM
>
> <HEM 357>: CAC HT3 CBC HC4
>
> <HEM 357>: C3C CBC CAC HV4
>
> <HEM 357>: CAB HT7 CBB HC8
>
> total 1310 improper torsions applied
>
> 26 improper torsions in old prep form
>
> Building H-Bond parameters.
>
> Not Marking per-residue atom chain types.
>
> Marking per-residue atom chain types.
>

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