Hi there,
I have a problem defining a ligand made of two components (inhibitor +
structural water).
Usually I had 1-198 - HIV-Protease as receptor and 199 - inhibitor as ligand
(and no structural water) and it worked fine.
Now I want to include a water into the calculation, one time as part of the
ligand and one time as part of the receptor and i can't find out how to do
it.
I'm trying to give enough information to desribe my problem (as far as I
understand my problem):
My topology for the simulation was made like this:
source leaprc.ff03
source leaprc.gaff
loadAmberParams apv.frcmod
rec=loadpdb rec.pdb
saveamberparm rec rec.top rec.crd
lig=loadmol2 apv.mol2
saveamberparm lig lig.top lig.crd
com=combine{rec lig}
saveamberparm com com.top com.crd
wat=loadpdb wat.pdb
sys=combine{com wat}
solvateOct sys TIP3PBOX 10
addions sys Cl- 0
saveamberparm sys com.TIP3PBOX.top com.TIP3PBOX.crd
The resulting numbering is
1-198 protein
199 ligand
200-204 chloride ions
205 water to be included in the MMPBSA calculation
206 ... many waters
So I'm trying
receptor_mask=:1-198
ligand_mask=:199:205
but of course I can't use the old com.top rec.top and lig.top because the
water is not in there.
So I'm trying to build new ones as follows:
source leaprc.ff03
source leaprc.gaff
loadAmberParams ../apv.frcmod
rec=loadpdb ../rec.pdb
lig=loadmol2 ../apv.mol2
wat=loadpdb ../wat.pdb
lig=combine{lig wat}
com=combine{rec lig}
saveamberparm rec rec.top rec.crd
savepdb rec rec.pdb
saveamberparm lig lig.top lig.crd
savepdb lig lig.pdb
saveamberparm com com.top com.crd
savepdb com com.pdb
If I now use these com.top rec.top and lig.top I get an error:
Preparing trajectories with ptraj...
1000 frames were read in and processed by ptraj for use in calculation.
Starting calculations...
Starting pb calculation...
calculating ligand contribution...
Unable to allocate memory!
(This often means you don't have enough memory available for this
calculation.)
VASSERT: ASSERTION FAILURE! filename vmem.c, line 249, (ram != ((void *)0))
sh: line 1: 30482 Abgebrochen /usr/local/amber11/bin/sander.APBS
-O -i _MMPBSA_pb.mdin -o _MMPBSA_ligand_pb.mdout -p lig.top -c
_MMPBSA_dummyligand.inpcrd -y _MMPBSA_ligand.mdcrd -r _MMPBSA_.restrt >>
_MMPBSA_pbsanderoutput.junk
calculating receptor contribution...
.... and so on ......
So, I have the impression that I do not really grep the water - and do not
know what happens there .
The _MMPBSA_cenptraj.in file reads as follows:
trajin ../prod.10ps_steps.mdcrd 1 1000 1
strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
center :1-198 mass origin
image origin center
center :1-200 mass origin
image origin center
rms first mass :1-198
average _MMPBSA_avgcomplex.pdb pdb
trajout _MMPBSA_complex.mdcrd nobox
How can I get the right com.top rec.top lig.top fitting to my simulation
data to do my calculation?
Thanks for any answers,
regards,
Oliver
Oliver Kuhn, Department of Bioinformatics,
Center for Medical Biotechnology, University of Duisburg-Essen,
Universitätsstr. 1-5, 45141 Essen, Germany
phone +49 201 183-3121, oliver.kuhn.uni-due.de
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Received on Thu Apr 21 2011 - 07:30:08 PDT
