Hi,
I would like to report on a subtle problem how leap handles protein systems
which contain
several chains.
What I have is a pdb structure of thrombin which has several breaks in the
protein chain,
which are separated by TER card in the original pdb file.
If I run this pdb file through leap (see the commands in a leap1.in command
file at the
bottom of this mail) and then use ambpdb to generate a pdb file from the
generated top and crd file, things look good, all TER cards in the generated
pdb files are
where I would expect them.
Now, if I remove the comment sign before the solvateoct command, and do the
exact same thing, the first TER
card in my pdb file disappears: in the leap-generated prot_1.pdb the TER card
between
ILE28 and ILE29 is present, however, when I generate a pdb file with
ambpdb -p prot_1.top < prot_1.crd > prot_bug.pdb
this TER card is missing.
I think it has to do with the contents of the "ATOMS_PER_MOLECULE" block in
the topology
file, which is written when solvate command is present where the first number
is the sum of
the atom counts of the first *two* chains.
Can someone confirm that this problem is real? I have attached the original
pdb file
1ahp.pdb and my leap1.in file.
The problem is that I use ptraj to convert my AMBER restart files into pdb
files for
further processing, and as the topology file does not reflect the chain
breaks properly,
the resulting pdb files do not have the appropriate TER cards, messing up my
downstream
processing.
Is there a workaround other than manually adding TER cards?
Thanks,
Th.
<<1ahp.pdb>> <<leap1.in>>
The leap commands I use are
# load forcefields
source leaprc.ff99SB
source leaprc.gaff
# load additional prepins, e.g. for ligands and ions
# load structure
COM = loadpdb "1ahp.pdb"
# vacuum topologies and coordinates
# solvate
#solvateoct COM TIP3PBOX 5
savepdb COM prot_1.pdb
saveamberparm COM prot_1.top prot_1.crd
quit
Mit freundlichen Grüßen / Kind regards,
Dr. Thomas Fox
Boehringer Ingelheim Pharma GmbH & Co. KG
Dept. Lead Identific. and Optim. Sup. Ge
Tel.: +49 (7351) 54-7585
Fax: +49 (7351) 83-7585
mailto:thomas.fox.boehringer-ingelheim.com
Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim
Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender),
Ralf Gorniak, Mark Hagmann, Michael Klein, Dr. Martin Wanning; Vorsitzender
des Aufsichtsrates: Prof. Dr. Dr. Andreas Barner; Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR B 23260
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- application/octet-stream attachment: 1ahp.pdb
- application/octet-stream attachment: leap1.in
Received on Tue Nov 29 2011 - 07:00:02 PST
