AMBER Archive (2004)

Subject: RE: AMBER: Problems with xleap

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Mar 01 2004 - 17:25:23 CST

Dear Xavi,

It would be useful if you could attach your rst and pdb files. I suspect,
however, that ptraj has either not preserved the residue names or has
wrapped the atom names. Try specifying the "nowrap" keyword on the end of
the pdb line in your ptraj input file. E.g

average file.pdb pdb nowrap

Also, try editing your pdb file and see if the residue names are incorrect.
If they are wrong then correct them. Do you have a residue called HHH? If
you do then you must have a lib/prep file for leap that defines this
residue, make sure you load that into leap 'before' you load the pdb.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Javier Perez Miron
> Sent: 26 February 2004 17:18
> To: amber_at_scripps.edu
> Subject: AMBER: Problems with xleap
>
> Hi everyone!!
>
> I made an optimization in vacuum using SANDER.So, I obtained
> many files. One of
> them is the .rst file. I converted that .rst file into .pdb
> file using the
> ptraj program. After that, I want to load the .pdb file using
> xleap. I don't
> know why but xleap generate other new atoms.
>
> In xleap, I write the next lines:
>
> loadoff unit_name library.lib
> unit_name = loadpdb pdb_file.pdb
>
> and the program write the follow lines:
>
> Loading PDB file: ./file.pdb
> Unknown residue: HHH number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: HHH number: 1 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: HHH number: 2 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: HHH number: 3 type: Nonterminal
> Unknown residue: HHH number: 4 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: HHH number: 5 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: HHH number: 6 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> and then,
>
> Creating new UNIT for residue: HHH sequence: 1
> ...
> Creating new UNIT for residue: HHH sequence: 2
> ...
> Creating new UNIT for residue: HHH sequence: 3
> ...
> Creating new UNIT for residue: HHH sequence: 4
> ...
> Creating new UNIT for residue: HHH sequence: 5
> ...
> Creating new UNIT for residue: HHH sequence: 6
> ...
>
>
> How can I resolve this problem?
>
> Best regards,
>
>
> Xavi Perez
>
> Chemoinformatic
> Universitat Autonoma de Barcelona
> Barcelona, Spain.
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