Aditi Borkar wrote:
Dear All,
Hello!
I am simulating a protein in a box of 9M acetic acid. I have obtained
the coordinates and gromacs topology for AcOH from PRODRG. The AcOH
has net -1 charge and the topology file is as follows:
PRODRG topologies generally produce unsatisfactory charges. For acetic acid, I
would use the same charges found in an ASP side chain as a starting point. You
will note that your topology differs greatly from an ASP side chain in any of
the Gromos96 force fields.
[ moleculetype ]
; Name nrexcl
ACA 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 ACA CAA 1 0.056 15.0350
2 C 1 ACA CAD 1 0.393 12.0110
3 OM 1 ACA OAC 1 -0.725 15.9994
4 OM 1 ACA OAB 1 -0.724 15.9994
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.153 334720.0 0.153 334720.0 ; CAA CAD
2 3 1 0.125 418400.0 0.125 418400.0 ; CAD OAC
2 4 1 0.125 418400.0 0.125 418400.0 ; CAD OAB
[ pairs ]
; ai aj fu c0, c1, ...
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 120.0 418.4 120.0 418.4 ; CAA CAD OAC
1 2 4 1 120.0 418.4 120.0 418.4 ; CAA CAD OAB
3 2 4 1 126.0 502.1 126.0 502.1 ; OAC CAD OAB
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 4 3 2 0.0 1673.6 0.0 1673.6 ; imp CAD
CAA OAB OAC
When I had tried taking uncharged AcOH, during equilibration, the
water and AcOH were completely segregating into two layers (like a
biphasic system).
My problem arises when I perform energy mimization on my solvated
protein. With 300 steps of EM (emtol 1000 and emstep .01) the EM
doesn't converge and more distrurbingly within these few steps, the
secondary structure of my protein is completely lost. This problem
does not occur when I do EM in box containing protein and pure water.
The Fmax is displayed onto 2 TRP residues.
It is strange that this degree of change is occurring during EM. But I wouldn't
try anything else until you're sure you are starting with reasonable parameters
(see above).
-Justin
My em.mdp file is as follows:
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 300
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
Please help!
Thank you!
-Aditi Borkar,
Tata Institute of Fundamental Research,
Mumbai,
India.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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