[gmx-users] trouble minimizing structure with mdrun

[Jack Shultz]

It seemed to run in NAMD with or without the infamous Fe4S4 center
gromacs with amber99SB or OPLSA with or without exotic species seems
to fail. Eventually I want to figure out this QM/MM integration with
MOPAC but that is a subject for later. Let me at least see if pure MM
works. I noticed that the solvation box I created using GROMACS did
not center the box on the protein. There was quite a big offset leave
more than half the molecule exposed. VMD did however solvate it right
on the center of mass. Even with the structure solvated, relaxed and
ionized gromacs failed.

Further effort I ran Zephyr which is a GUI integration with
OpenMMGromacs. That uses amber96 and implicit solvent. The application
seems to run, but I was not able to load any trajectories and obtain
further data to analyze the results.

On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Jack,
>
> Can you be more specific? A quick glance at 1YQW shows that there's
> quite a bit of exotic stuff, including several times the infamous
> Fe4S4 center. How did you deal with that? At first instance, what
> protocol did you used, and what error did you get (and at which
> point)?
> After preparation with (V|NA)MD, did pdb2gmx correctly assign chains,
> or did it tie chains together? In the latter case it would have issued
> a number of "Long Bond Warnings". Did everything else odd show up in
> the output of any of those steps? Did you actually read through it?
>
> Cheers,
>
> Tsjerk
>
> On Mon, Jan 4, 2010 at 1:38 AM, Jack Shultz <js at drugdiscoveryathome.com> wrote:
>> I've been having trouble minimizing a structure using gromacs so I
>> decided to try using another MD app and see if I can generate a more
>> relaxed structure.
>> Using VMD & NAMD I was able to minimize and run MD for this structure
>> from RCSB.ORG 1YQW.pdb. It was solvated and ionized.
>>
>> I then took the last frame from a 10,000 step trajectory and exported
>> it into a pdb file. I preped it so it was compatible with amber99sb
>> port for gromacs
>> read it into tleap using amebr99sb and wrote a pdb file from that
>> Then fixed residues so it it was compatible with gromac
>>
>> pdb2gmx -ff amber99sb -f protein2.pdb -water spce -ignh
>> editconf -bt triclinic -f conf.gro -d 1.0
>> genbox -cp out.gro -cs ffamber_tip3p.gro
>> grompp -f em.mdp
>> echo 13 |genion -s topol.tpr -neutral -conc 0.15 -p topol.top
>> grompp -f em.mdp -c out.gro
>> mdrun -s topol.tpr -v
>>
>> Back Off! I just backed up md.log to ./#md.log.2#
>> Getting Loaded...
>> Reading file topol.tpr, VERSION 4.0.5 (single precision)
>> Loaded with Money
>>
>>
>> Back Off! I just backed up traj.trr to ./#traj.trr.2#
>>
>> Back Off! I just backed up ener.edr to ./#ener.edr.2#
>> Polak-Ribiere Conjugate Gradients:
>>   Tolerance (Fmax)   =  2.00000e+02
>>   Number of steps    =        10000
>>   F-max             =  2.97876e+06 on atom 16106
>>   F-Norm            =  2.59700e+04
>>
>> Step 0, Epot=4.125301e+07, Fnorm=2.399e+04, Fmax=2.975e+06 (atom 16106)
>> Step 1, Epot=4.111934e+07, Fnorm=2.285e+04, Fmax=2.969e+06 (atom 16106)
>> Step 2, Epot=4.092903e+07, Fnorm=2.216e+04, Fmax=2.959e+06 (atom 16106)
>>
>> ....
>>
>> Step 127, Epot=7.765358e+06, Fnorm=1.020e+05, Fmax=2.836e+07 (atom 28298)
>> Step 128, Epot=1.606771e+08, Fnorm=6.739e+07, Fmax=1.876e+10 (atom 10310)
>> Step 129, Epot=5.454451e+09, Fnorm=4.339e+09, Fmax=1.179e+12 (atom 36500)
>> There were 2 inconsistent shifts. Check your topology
>>
>>
>>
>>
>> em.mdp parameters
>> define = -DFLEXIBLE
>> integrator = cg
>> nsteps = 10000
>> constraints = none
>> emtol = 200.0
>> nstcgsteep = 10 ; do a steep every 10 steps of cg
>> emstep = 0.01 ; used with steep
>> nstcomm = 1
>> coulombtype = PME
>> ns_type = grid
>> rlist = 1.0
>> rcoulomb = 1.0
>> rvdw = 1.4
>> Tcoupl = no
>> Pcoupl = no
>> gen_vel = no
>> nstxout = 0 ; write coords every # step
>> optimize_fft = yes
>> table-extension = 100
>> ld_seed = -1
>>
>>
>> --
>> Jack
>>
>> http://drugdiscoveryathome.com
>> http://hydrogenathome.org
>> --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org