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.war...@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.war...@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-boun...@gromacs.org [mailto: > gmx-users-boun...@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 : monu46...@yahoo.com**** > > ** ** > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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 : monu46...@yahoo.com
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists