Hi,
On Mon, Dec 1, 2014 at 3:00 PM, Aronica, Pietro
<pietro.aronica07.imperial.ac.uk> wrote:
due to the faulty pdb. Extracting the pdb with cpptraj (simple trajin
restart/trajout pdb) from the final restart file (which contains
100799 atoms, as per header) gives a pdb with 100800 atoms and 30840
residues, whereas the prmtop had 100799 and 30837. This does not occur
if the pdb size is underneath 100000. Extracting the pdb with ambpdb
gives a pdb with the correct number of atoms and residues, and works
fine with those CONECT records.
What version of cpptraj are you using? If it's the latest version
(V14.22) can you send me your PDB off-list so I can try to reproduce
the problem? Thanks.
-Dan
>
> I can go through the faulty pdb and try to figure out where the extra atom and three extra residues come from, but I was hoping at this point there'd be a solution that doesn't involve me poring over hundreds of thousands of lines of pdb file.
>
> Pietro
> ________________________________________
> From: David A Case [case.biomaps.rutgers.edu]
> Sent: 01 December 2014 12:36
> To: AMBER Mailing List
> Subject: Re: [AMBER] LEaP Error
>
> On Mon, Dec 01, 2014, Aronica, Pietro wrote:
>
>> I'm having problems with LEaP. It has problems loading some perfectly
>> fine pdb files, because, I suspect, they have more than 100000 atoms. In
>> particular, I think it is misinterpreting the CONECT data of the
>> disulphide bridges, trying to link cysteines to water molecules and
>> crashing out after having an ATOMS NOT BONDED fatal error.
>
> We need more information than this. There is no particular reason why
> leap should fail with systems larger than 100000 atoms. Do the CONECT
> records go beyond that limit? PDB files allocate six digits for the atom
> number, so generally only have problems with more than a million atoms.
>
> There may well be instances where LEaP messes up parsing of CONECT data.
> You will probably have to post a file that illustrates the problem. Be sure
> that you have converted CYS residues to CYX.
>
> ....dac
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Dec 01 2014 - 14:30:03 PST
