[gmx-users] Re: Increase in charge after adding the ligand

Tue Jun 21 04:31:29 CEST 2011

I checked the .gro file , in that only 9 NA are mentioned.. also during the
minimization step I am getting the following error:-

step 100: Water molecule starting at atom 85940 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  100, Dmax= 2.4e-01 nm, Epot= -4.86897e+06 Fmax= 2.60577e+06, atom=
85940
Step=  101, Dmax= 2.8e-01 nm, Epot= -4.88265e+06 Fmax= 1.03794e+05, atom=
3628

step 102: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  102, Dmax= 3.4e-01 nm, Epot=  7.97834e+06 Fmax= 1.57210e+09, atom=
3631
step 103: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  104, Dmax= 8.5e-02 nm, Epot= -4.90566e+06 Fmax= 2.85624e+05, atom=
3628
Step=  105, Dmax= 1.0e-01 nm, Epot= -4.91390e+06 Fmax= 1.97964e+05, atom=
3628

step 106: Water molecule starting at atom 125885 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  107, Dmax= 6.2e-02 nm, Epot= -4.92487e+06 Fmax= 6.32096e+04, atom=
362885
Step=  108, Dmax= 7.4e-02 nm, Epot= -4.95276e+06 Fmax= 4.18514e+04, atom=
3627
Step=  109, Dmax= 8.9e-02 nm, Epot= -4.98566e+06 Fmax= 1.91771e+05, atom=
3620
Step=  110, Dmax= 1.1e-01 nm, Epot= -5.00651e+06 Fmax= 1.56721e+05, atom=
3620
Step=  112, Dmax= 6.4e-02 nm, Epot= -5.01376e+06 Fmax= 1.25375e+05, atom=
3620
Step=  113, Dmax= 7.7e-02 nm, Epot= -5.02950e+06 Fmax= 5.35431e+04, atom=
3620
Step=  114, Dmax= 9.2e-02 nm, Epot= -5.04978e+06 Fmax= 2.03884e+05, atom=
3620
Step=  115, Dmax= 1.1e-01 nm, Epot= -5.07406e+06 Fmax= 6.55437e+04, atom=
3620
Step=  116, Dmax= 1.3e-01 nm, Epot= -5.10420e+06 Fmax= 4.48874e+05, atom=
3620
Step=  117, Dmax= 1.6e-01 nm, Epot= -5.11132e+06 Fmax= 1.89966e+05, atom=
3620

step 118: Water molecule starting at atom 213098 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  118, Dmax= 1.9e-01 nm, Epot= -5.12615e+06 Fmax= 2.25039e+05, atom=
3620

step 119: Water molecule starting at atom 252632 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 119: Water molecule starting at atom 212687 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step=  119, Dmax= 2.3e-01 nm, Epot= -5.15014e+06 Fmax= 1.78972e+07, atom=
212687
Step=  120, Dmax= 2.7e-01 nm, Epot= -5.15139e+06 Fmax= 9.55607e+04, atom=
3620

step 121: Water molecule starting at atom 171371 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  122, Dmax= 1.6e-01 nm, Epot= -5.16214e+06 Fmax= 3.02686e+05, atom=
3620
Step=  123, Dmax= 2.0e-01 nm, Epot= -5.18637e+06 Fmax= 1.61921e+05, atom=
3620
Step=  124, Dmax= 2.4e-01 nm, Epot= -5.21873e+06 Fmax= 7.51816e+04, atom=
3620

step 125: Water molecule starting at atom 213098 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  125, Dmax= 2.8e-01 nm, Epot= -5.13297e+06 Fmax= 1.02333e+08, atom=
212927
step 126: Water molecule starting at atom 212927 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  126, Dmax= 1.4e-01 nm, Epot= -5.23551e+06 Fmax= 2.01165e+05, atom=
3620
Step=  127, Dmax= 1.7e-01 nm, Epot= -5.25949e+06 Fmax= 9.03334e+04, atom=
3620
Step=  129, Dmax= 1.0e-01 nm, Epot= -5.27727e+06 Fmax= 1.03222e+05, atom=
3620
Step=  130, Dmax= 1.2e-01 nm, Epot= -5.29146e+06 Fmax= 1.41302e+05, atom=
3630
Step=  132, Dmax= 7.4e-02 nm, Epot= -5.30238e+06 Fmax= 7.19601e+04, atom=
3630
Step=  133, Dmax= 8.8e-02 nm, Epot= -5.32013e+06 Fmax= 5.75864e+04, atom=
3630
Step=  134, Dmax= 1.1e-01 nm, Epot= -5.33172e+06 Fmax= 1.98591e+05, atom=
3622
Step=  135, Dmax= 1.3e-01 nm, Epot= -5.34273e+06 Fmax= 1.20478e+05, atom=
3622
Step=  136, Dmax= 1.5e-01 nm, Epot= -5.36395e+06 Fmax= 7.56979e+04, atom=
3620
Step=  138, Dmax= 9.2e-02 nm, Epot= -5.37722e+06 Fmax= 7.34765e+04, atom=
3622
Step=  139, Dmax= 1.1e-01 nm, Epot= -5.38280e+06 Fmax= 2.57798e+05, atom=
3622
Step=  140, Dmax= 1.3e-01 nm, Epot= -5.39328e+06 Fmax= 5.13241e+05, atom=
3622

step 141: Water molecule starting at atom 171395 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  142, Dmax= 7.9e-02 nm, Epot= -5.40360e+06 Fmax= 5.65055e+04, atom=
362295
Step=  143, Dmax= 9.5e-02 nm, Epot= -5.42336e+06 Fmax= 6.92127e+04, atom=
3620
Step=  144, Dmax= 1.1e-01 nm, Epot= -5.42672e+06 Fmax= 3.08454e+05, atom=
3620
Step=  145, Dmax= 1.4e-01 nm, Epot= -5.44497e+06 Fmax= 8.28412e+04, atom=
3620
Step=  146, Dmax= 1.6e-01 nm, Epot= -5.45986e+06 Fmax= 1.68180e+05, atom=
3620
Step=  147, Dmax= 2.0e-01 nm, Epot= -5.47710e+06 Fmax= 6.39076e+04, atom=
3620
Step=  150, Dmax= 5.9e-02 nm, Epot= -5.49010e+06 Fmax= 7.14589e+04, atom=
3620
Step=  151, Dmax= 7.1e-02 nm, Epot= -5.50033e+06 Fmax= 6.50889e+04, atom=
3631
Step=  152, Dmax= 8.5e-02 nm, Epot= -5.51008e+06 Fmax= 9.01451e+04, atom=
3631
Step=  153, Dmax= 1.0e-01 nm, Epot= -5.51782e+06 Fmax= 1.14429e+05, atom=
3631
Step=  154, Dmax= 1.2e-01 nm, Epot= -5.52769e+06 Fmax= 1.10653e+05, atom=
3631
Step=  155, Dmax= 1.5e-01 nm, Epot= -5.53537e+06 Fmax= 8.81568e+04, atom=
3631
Step=  157, Dmax= 8.8e-02 nm, Epot= -5.54703e+06 Fmax= 1.72202e+05, atom=
3627
Step=  158, Dmax= 1.1e-01 nm, Epot= -5.55035e+06 Fmax= 5.92969e+05, atom=
3627
Step=  159, Dmax= 1.3e-01 nm, Epot= -5.55740e+06 Fmax= 9.21361e+04, atom=
3627
Step=  161, Dmax= 7.6e-02 nm, Epot= -5.56682e+06 Fmax= 4.70994e+04, atom=
3627
Step=  162, Dmax= 9.2e-02 nm, Epot= -5.58254e+06 Fmax= 4.61149e+04, atom=
3627
Step=  163, Dmax= 1.1e-01 nm, Epot= -5.58425e+06 Fmax= 2.41217e+05, atom=
3627
Step=  164, Dmax= 1.3e-01 nm, Epot= -5.60094e+06 Fmax= 1.54088e+05, atom=
3627
Step=  165, Dmax= 1.6e-01 nm, Epot= -5.60984e+06 Fmax= 1.35631e+05, atom=
3627
Step=  166, Dmax= 1.9e-01 nm, Epot= -5.62023e+06 Fmax= 8.55147e+04, atom=
3627
Step=  168, Dmax= 1.1e-01 nm, Epot= -5.63209e+06 Fmax= 8.17613e+04, atom=
3627
Step=  169, Dmax= 1.4e-01 nm, Epot= -5.64107e+06 Fmax= 8.85408e+04, atom=
3627
Step=  171, Dmax= 8.2e-02 nm, Epot= -5.65284e+06 Fmax= 5.15772e+04, atom=
3627
Step=  172, Dmax= 9.8e-02 nm, Epot= -5.65812e+06 Fmax= 1.01666e+05, atom=
3628
Step=  173, Dmax= 1.2e-01 nm, Epot= -5.66262e+06 Fmax= 1.88903e+05, atom=
3628
Step=  174, Dmax= 1.4e-01 nm, Epot= -5.67125e+06 Fmax= 1.44782e+05, atom=
3628

step 175: Water molecule starting at atom 86381 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=  175, Dmax= 1.7e-01 nm, Epot= -5.67920e+06 Fmax= 2.18421e+05, atom=
86381
Step=  193, Dmax= 1.6e-06 nm, Epot= -5.66548e+06 Fmax= 4.55942e+05, atom=
125963
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 194 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -5.6791960e+06
Maximum force     =  2.1842059e+05 on atom 86381
Norm of force     =  5.6555481e+02

On Tue, Jun 21, 2011 at 11:10 AM, Dallas Warren <Dallas.Warren at monash.edu>wrote:

>  You need to work out exactly why you have the mis-match, something is
> screwy.****
>
> ** **
>
> Something that you are doing does not add up.****
>
> ** **
>
> What is the charge on the ligand?  Appears to be -7.****
>
> ** **
>
> Why when you add 9 Na+ do you then end up with a charge of +8?  Seems that
> you have actually added 17 sodiums from those numbers.****
>
> ** **
>
> Catch ya,
>
> Dr. Dallas Warren****
>
> Medicinal Chemistry and Drug Action****
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu****
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail. ****
>
> ** **
>
> *From:* gmx-users-bounces at gromacs.org [mailto:
> gmx-users-bounces at gromacs.org] *On Behalf Of *bharat gupta
> *Sent:* Tuesday, 21 June 2011 12:05 PM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Re: Increase in charge after adding the ligand****
>
> ** **
>
> Hi,
>
> Initially while preparing the structure , -2 charge was there on the
> protein. Next, after adding the ligand and executing grompp statement It
> showing -9.9 charge. So I added 9 sodium ions. but still its showing +8
> charge on the system. what shall I do in this case ??
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343****
>
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com****
>
> ** **
>
> --
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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