Thank you David, you are right.
but it seems there is something else
top2mol2 adds a number to the residue name. can i control that with a flag?
Quoting "David A. Case" <case.biomaps.rutgers.edu>:
> On Tue, Apr 07, 2009, taufik.alsarraj.utoronto.ca wrote:
>
>> I am using top2mol2 to convert amber files *.prmtop (*.inpcrd or *.rst)
>> to create mol2 files. I notice that my residue names are changing every
>> time i do this.
>
>> In the original mol2 file, the residues are Sur, Smcc, A5 DT DT etc
>> after salvation with xleap and a minimization with sander i use top2mol2
>> to create a new mol2 file. I found the reason why my residue names are
>> changing is because in *.prmtop file only three characters are used for
>> residues.
>
> Sounds like this is the problem. The pdb format (for biomolecules) only
> allows three characters for atom names, and LEaP conversion probably
> maintains this restriction. (Generally, PDB-format files, rather than
> mol2 format files, are used for input to LEaP). I'm not sure that it
> is easy to have residue names in Amber more than three characters long,
> although there is no fundamental reason for this -- just that we would
> have figure out what to do when asked to write PDB files if the names are
> longer than that allowed.
>
> You could try building the prmtop file with sleap, to see what
> happens....but you should also consider if there is any way to use
> three-letter residue names exclusively.
>
> ....good luck....dac
>
>
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Received on Wed Apr 08 2009 - 01:20:31 PDT
