On 2/15/17 1:46 PM, Dayhoff, Guy wrote:
Hi,
Thanks for taking the time to humor my inquiry.
I’m hoping to find a fix for my issue or obtain a working beta-D-glucose
monomer model that I can use to
continue troubleshooting my issue. Details below… (This is my first
post, forgive me for including too much/
too little context)
My Best,
Guy Dayhoff
I am attempting to employ the Drude-2013FF available below to use with some
carbohydrates:
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/drude-2013b_16sep2016.tgz
I have obtained and installed the DRUDE compatible GROMACS distro available
via:
git clone git://git.gromacs.org/gromacs.git
cd gromacs
git checkout drude
I am using pre-equilibrated SWM4-NDP water available from:
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/swm4-ndp_1024.gro
I have adjusted Drude parameters in my mdp files as demonstrated in the
additional material from the publication
regarding implementation of the Drude FF and extended Lagrangian dynamics
in GROMACS.
Publication: http://dx.doi.org/10.1002/jcc.23937
; DRUDE PARAMETERS
drude = yes
drude-mode = SCF
drude-hyper = yes
drude-khyp = 16736000.0
drude-r = 0.02
drude-pow = 4
I prepared a Drude model of beta-D-glucose(BGLC) to run before using more
complex models by:
Downloading .CIF and .SDF data from RCSB-PDB @ https://www3.rcsb.org/ligand/BGC
Feeding this data into the CHARMM-GUI’s Ligand Reader & Modeler to produce .PDB
and .PSF files
Feeding the .PDB and .PSF files into the CHARMM-GUI’s Drude Prepper producing
bDgluc-Drude.pdb
I generated a topology file with pdb2gmx without any warnings/notes/errors:
gmx pdb2gmx -f bDgluc-Drude.pdb -o bDgluc-Drude.gro -p bDgluc-Drude.top
I placed the BGLC model in the center of a 3.0 x 3.0 x 3.0 box and
minimized successfully:
gmx editconf -f bDgluc-Drude.gro -o bDgluc-Drude-CEN.gro -box 3.0 3.0 3.0
-center 1.5 1.5 1.5
gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-CEN.gro -p
bDgluc-Drude.top -o bDgluc-Drude-EMV.tpr
gmx mdrun -v -deffnm bDgluc-Drude-EMV
I then solvate the system and attempt to minimize it once more, this
results in a seg fault 11:
gmx solvate -cp bDgluc-Drude-EMV.gro -cs swm4-ndp.gro -p bDgluc-Drude.top -o
bDgluc-Drude-SOL.gro
gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-SOL.gro -p
bDgluc-Drude.top -o bDgluc-Drude-EMS.tpr
gmx mdrun -v -deffnm bDgluc-Drude-EMS
Step= 0, Dmax= 1.0e-02 nm, Epot= nan Fmax= 3.77896e+06, atom= 16
Segmentation fault: 11
Likewise, if I simply take the minimized BGLC and attempt to minimize a
second time I get the seg fault 11:
gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-EMV.gro -p
bDgluc-Drude.top -o bDgluc-Drude-EMV2.tpr
gmx mdrun -v -deffnm bDgluc-Drude-EMV2
Step= 0, Dmax= 1.0e-03 nm, Epot= nan Fmax= 1.95057e+04, atom= 11
Segmentation fault: 11
I have attempted to isolate the cause and have noted:
minimization and subsequent runs of a box of pure swm4-ndp produces no
such errors, indicating the issue
is most likely related to the BGLC molecule in the system.
when beginning with a beta-D-glucose model not prepared with the CHARMM-GUI
Drude Prepper (i.e. without
lone pairs and drudes included in the coordinate file) pdb2gmx properly
adds all drudes, however fails to add
LP5A and LP5B, LPX5 is added though (CHARMM-GUI’s Drude Prepper doesn’t
appear to have this issue).
using the -missing flag and proceeding with minimzation, solvation, NVT
and NPT ensembles using the incomplete
model does not cause any seg faults and completes without errors. In
this case however, the molecule has a charge
(which corresponds exactly to the missing LP5A and LP5B).
with all things considered, I believe the issue lies with the handling of
LP5A/LP5B in the BGLC residue in my model
but am unsure of how to proceed at this point.
It appears that LP5A and LP5B are missing from the .rtp definition so indeed
they will not be built and the exclusions, etc. will be wrong. I didn't test
all the carbohydrates yet so I don't know why this occurred.
I'll look into it.
-Justin
the seg fault: 11 occurs on the first step of the minimizations
My complete min.mdp for reference:
; PREPROCESSING
define =
; RUN CONTROL
integrator = steep
nsteps = 10000
dt = 0.001
comm-mode = Linear
nstcomm = 1
nstcalcenergy = 1
; NEIGHBORSEARCHING
ns-type = grid
rlist = 1.2
pbc = xyz
cutoff-scheme = Verlet
periodic-molecules = no
; BONDS
constraints = none
continuation = no
; ELECTROSTATICS AND VDW
coulombtype = PME
rcoulomb = 1.2
vdwtype = Cut-off
rvdw = 1.2
DispCorr = EnerPres
vdw-modifier = potential-switch
rvdw-switch = 1.0
; ENERGY MINIMIZATION OPTIONS
emtol = 10.0
emstep = 0.001
; EWALD
fourierspacing = 0.1
pme_order = 4
ewald_rtol = 1e-5
ewald_geometry = 3d
; DRUDE PARAMETERS
drude = yes
drude-mode = SCF
drude-hyper = yes
drude-khyp = 16736000.0
drude-r = 0.02
drude-pow = 4
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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