So, after adding 1 NA ion, I started with energy mimization, but I am getting the following error after md run command :-<br><br>Step= 1, Dmax= 1.0e-02 nm, Epot= 1.36889e+09 Fmax= 1.97591e+11, atom= 1248<br>Step= 2, Dmax= 1.2e-02 nm, Epot= 5.46814e+07 Fmax= 3.57239e+09, atom= 972<br>
Step= 3, Dmax= 1.4e-02 nm, Epot= 8.68244e+06 Fmax= 5.80655e+08, atom= 1253<br>Step= 4, Dmax= 1.7e-02 nm, Epot= 3.33619e+06 Fmax= 9.98000e+07, atom= 1248<br>Step= 5, Dmax= 2.1e-02 nm, Epot= 2.30163e+06 Fmax= 1.19057e+07, atom= 1253<br>
Step= 6, Dmax= 2.5e-02 nm, Epot= 2.07254e+06 Fmax= 3.20568e+06, atom= 1304<br>Step= 7, Dmax= 3.0e-02 nm, Epot= 1.97667e+06 Fmax= 1.59513e+06, atom= 1045<br>Step= 8, Dmax= 3.6e-02 nm, Epot= 1.85877e+06 Fmax= 8.25518e+05, atom= 3616<br>
Step= 9, Dmax= 4.3e-02 nm, Epot= 1.66148e+06 Fmax= 7.69483e+05, atom= 3616<br>Step= 10, Dmax= 5.2e-02 nm, Epot= 1.43976e+06 Fmax= 6.47087e+05, atom= 3616<br>Step= 11, Dmax= 6.2e-02 nm, Epot= 1.16869e+06 Fmax= 6.39015e+05, atom= 3616<br>
Step= 12, Dmax= 7.4e-02 nm, Epot= 8.84664e+05 Fmax= 5.75494e+05, atom= 3616<br>Step= 13, Dmax= 8.9e-02 nm, Epot= 6.62825e+05 Fmax= 1.01984e+07, atom= 47956<br><br>step 14: Water molecule starting at atom 47956 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>Wrote pdb files with previous and current coordinates<br>Step= 15, Dmax= 5.3e-02 nm, Epot= 5.67330e+05 Fmax= 5.36987e+05, atom= 36166<br>Step= 16, Dmax= 6.4e-02 nm, Epot= 3.51341e+05 Fmax= 4.19647e+05, atom= 3619<br>
Step= 17, Dmax= 7.7e-02 nm, Epot= 6.34731e+04 Fmax= 1.56555e+06, atom= 3616<br>Step= 18, Dmax= 9.2e-02 nm, Epot= -2.03364e+04 Fmax= 4.60916e+05, atom= 3616<br>Step= 19, Dmax= 1.1e-01 nm, Epot= -3.50504e+05 Fmax= 1.53090e+06, atom= 213514<br>
<br>step 20: Water molecule starting at atom 213514 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>Wrote pdb files with previous and current coordinates<br>Step= 20, Dmax= 1.3e-01 nm, Epot= -4.11692e+05 Fmax= 4.49357e+05, atom= 3619<br>
Step= 21, Dmax= 1.6e-01 nm, Epot= -4.87207e+05 Fmax= 3.39700e+07, atom= 3629<br>Step= 22, Dmax= 1.9e-01 nm, Epot= -7.85503e+05 Fmax= 3.56083e+05, atom= 3619<br><br>step 23: Water molecule starting at atom 206593 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br><br>step 23: Water molecule starting at atom 212776 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>Step= 23, Dmax= 2.3e-01 nm, Epot= 1.95863e+09 Fmax= 6.76309e+11, atom= 3633<br>step 24: Water molecule starting at atom 212776 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>Step= 25, Dmax= 5.8e-02 nm, Epot= -9.28980e+05 Fmax= 2.81692e+05, atom= 362976<br><br>step 26: Water molecule starting at atom 42463 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>Step= 27, Dmax= 3.5e-02 nm, Epot= -1.03111e+06 Fmax= 2.76677e+05, atom= 36293<br>Step= 28, Dmax= 4.1e-02 nm, Epot= -1.14733e+06 Fmax= 2.66398e+05, atom= 3629<br>
Step= 29, Dmax= 5.0e-02 nm, Epot= -1.26821e+06 Fmax= 2.51779e+05, atom= 3629<br>Step= 30, Dmax= 6.0e-02 nm, Epot= -1.42873e+06 Fmax= 2.31393e+05, atom= 3629<br>Step= 31, Dmax= 7.2e-02 nm, Epot= -1.59623e+06 Fmax= 3.53379e+06, atom= 3633<br>
<br>step 32: Water molecule starting at atom 292885 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>Wrote pdb files with previous and current coordinates<br>Step= 33, Dmax= 4.3e-02 nm, Epot= -1.62300e+06 Fmax= 2.45780e+05, atom= 361985<br>
Step= 34, Dmax= 5.2e-02 nm, Epot= -1.75124e+06 Fmax= 2.87155e+05, atom= 213958<br>Step= 35, Dmax= 6.2e-02 nm, Epot= -1.86014e+06 Fmax= 6.76483e+05, atom= 3634<br><br>step 36: Water molecule starting at atom 256024 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>Wrote pdb files with previous and current coordinates<br>Step= 36, Dmax= 7.4e-02 nm, Epot= -1.91639e+06 Fmax= 2.49523e+05, atom= 3619<br>Step= 37, Dmax= 8.9e-02 nm, Epot= -2.11154e+06 Fmax= 4.87466e+05, atom= 3636<br>
Step= 38, Dmax= 1.1e-01 nm, Epot= -2.20858e+06 Fmax= 1.92308e+05, atom= 3629<br>Step= 40, Dmax= 6.4e-02 nm, Epot= -2.34036e+06 Fmax= 3.07614e+06, atom= 3634<br>Step= 41, Dmax= 7.7e-02 nm, Epot= -2.36181e+06 Fmax= 1.95100e+05, atom= 3634<br>
Step= 42, Dmax= 9.2e-02 nm, Epot= -2.55367e+06 Fmax= 1.66837e+05, atom= 3629<br>Step= 43, Dmax= 1.1e-01 nm, Epot= -2.67052e+06 Fmax= 1.01067e+07, atom= 3618<br>Step= 44, Dmax= 1.3e-01 nm, Epot= -2.76975e+06 Fmax= 2.25183e+05, atom= 3618<br>
Step= 45, Dmax= 1.6e-01 nm, Epot= -2.95070e+06 Fmax= 5.66364e+05, atom= 3614<br><br>step 46: Water molecule starting at atom 249877 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
<br>step 46: Water molecule starting at atom 85966 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates<br>
Step= 46, Dmax= 1.9e-01 nm, Epot= -2.97755e+06 Fmax= 9.94270e+06, atom= 249877<br>Step= 47, Dmax= 2.3e-01 nm, Epot= -2.99471e+06 Fmax= 2.40481e+05, atom= 3614<br>Step= 48, Dmax= 2.8e-01 nm, Epot= -3.24066e+06 Fmax= 2.63430e+06, atom= 3608<br>
<br>step 49: Water molecule starting at atom 82687 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br><br>step 49: Water molecule starting at atom 129469 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates<br>Step= 49, Dmax= 3.3e-01 nm, Epot= 1.19344e+08 Fmax= 1.97429e+10, atom= 3608<br>step 50: Water molecule starting at atom 129469 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>Wrote pdb files with previous and current coordinates<br>Step= 51, Dmax= 8.3e-02 nm, Epot= -3.28700e+06 Fmax= 3.42115e+05, atom= 3620<br>Step= 52, Dmax= 9.9e-02 nm, Epot= -3.35221e+06 Fmax= 5.71868e+05, atom= 3620<br>
<br>step 53: Water molecule starting at atom 82687 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>Wrote pdb files with previous and current coordinates<br>Step= 53, Dmax= 1.2e-01 nm, Epot= -3.37935e+06 Fmax= 2.23519e+05, atom= 3620<br>
Step= 54, Dmax= 1.4e-01 nm, Epot= -3.48138e+06 Fmax= 1.24343e+06, atom= 3620<br><br>step 55: Water molecule starting at atom 82687 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>Step= 55, Dmax= 1.7e-01 nm, Epot= -3.47365e+06 Fmax= 4.00718e+07, atom= 82687<br>step 56: Water molecule starting at atom 82687 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>Step= 56, Dmax= 8.6e-02 nm, Epot= -3.49998e+06 Fmax= 1.67258e+05, atom= 3620<br>Step= 57, Dmax= 1.0e-01 nm, Epot= -3.59531e+06 Fmax= 9.54825e+04, atom= 3634<br>
Step= 59, Dmax= 6.2e-02 nm, Epot= -3.67520e+06 Fmax= 4.07963e+05, atom= 3622<br>Step= 60, Dmax= 7.4e-02 nm, Epot= -3.69432e+06 Fmax= 1.64972e+05, atom= 3622<br>Step= 61, Dmax= 8.9e-02 nm, Epot= -3.75825e+06 Fmax= 2.68322e+05, atom= 3613<br>
Step= 62, Dmax= 1.1e-01 nm, Epot= -3.78424e+06 Fmax= 2.62259e+05, atom= 3613<br>Step= 63, Dmax= 1.3e-01 nm, Epot= -3.84569e+06 Fmax= 2.41290e+05, atom= 3622<br>Step= 64, Dmax= 1.5e-01 nm, Epot= -3.84643e+06 Fmax= 2.38963e+06, atom= 3622<br>
Step= 65, Dmax= 1.8e-01 nm, Epot= -3.87919e+06 Fmax= 5.87824e+05, atom= 3622<br>Step= 66, Dmax= 2.2e-01 nm, Epot= -3.94983e+06 Fmax= 8.25176e+04, atom= 3634<br><br>step 67: Water molecule starting at atom 170884 can not be settled.<br>
Check for bad contacts and/or reduce the timestep if appropriate.<br>Wrote pdb files with previous and current coordinates<br>Step= 69, Dmax= 6.6e-02 nm, Epot= -4.00963e+06 Fmax= 4.49243e+05, atom= 3607<br>Step= 70, Dmax= 8.0e-02 nm, Epot= -4.02678e+06 Fmax= 1.17113e+05, atom= 3607<br>
Step= 71, Dmax= 9.6e-02 nm, Epot= -4.07699e+06 Fmax= 7.52519e+05, atom= 3614<br><br>step 72: Water molecule starting at atom 212809 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>Step= 72, Dmax= 1.1e-01 nm, Epot= -4.07756e+06 Fmax= 1.16158e+06, atom= 3614<br>Step= 73, Dmax= 1.4e-01 nm, Epot= -4.10951e+06 Fmax= 1.30165e+05, atom= 3613<br>
Step= 74, Dmax= 1.7e-01 nm, Epot= -4.14116e+06 Fmax= 4.07543e+06, atom= 3613<br><br>step 75: Water molecule starting at atom 212809 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>Step= 75, Dmax= 2.0e-01 nm, Epot= -4.18383e+06 Fmax= 8.70248e+05, atom= 212809<br>Step= 76, Dmax= 2.4e-01 nm, Epot= -4.20933e+06 Fmax= 1.39623e+05, atom= 3613<br>
Step= 78, Dmax= 1.4e-01 nm, Epot= -4.26151e+06 Fmax= 9.65736e+05, atom= 3613<br><br>step 79: Water molecule starting at atom 212809 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>Step= 79, Dmax= 1.7e-01 nm, Epot= -4.26416e+06 Fmax= 9.92323e+05, atom= 212809<br>Step= 80, Dmax= 2.1e-01 nm, Epot= -4.28752e+06 Fmax= 1.65125e+05, atom= 3613<br>
Step= 81, Dmax= 2.5e-01 nm, Epot= -4.35502e+06 Fmax= 8.28132e+05, atom= 3613<br><br>step 82: Water molecule starting at atom 212809 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>Step= 82, Dmax= 3.0e-01 nm, Epot= -1.93670e+06 Fmax= 2.75398e+08, atom= 3607<br>step 83: Water molecule starting at atom 212809 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br>Step= 83, Dmax= 1.5e-01 nm, Epot= -4.36885e+06 Fmax= 3.77499e+09, atom= 212809<br>Step= 84, Dmax= 1.8e-01 nm, Epot= -4.36949e+06 Fmax= 4.70130e+05, atom= 3607<br>
Step= 85, Dmax= 2.1e-01 nm, Epot= -4.39550e+06 Fmax= 6.53132e+05, atom= 3607<br><br>step 86: Water molecule starting at atom 129571 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
Wrote pdb files with previous and current coordinates<br><br><br><br><div class="gmail_quote">On Tue, Jun 21, 2011 at 3:15 PM, bharat gupta <span dir="ltr"><<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">I fixed it ... but now after using the command : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr <br><br>I am getting a charge of -9.999971e-01<br>
<br><br>Since the charge has to be in whole number, what shall I do in this case. (The ligand that I am using is phosphotyrosine)<div><div></div><div class="h5"><br>
<br><br><div class="gmail_quote">On Tue, Jun 21, 2011 at 2:13 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>On 21/06/2011 3:03 PM, bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Now I changed the .top file in this way and I am getting this error now :-<br>
<br>
change :- ; Include forcefield parameters<br>
#include "charmm27.ff/forcefield.itp"<br>
<br>
;Include ligand topology<br>
#include "PTR.itp"<br>
<br>
[ moleculetype ]<br>
; Name nrexcl<br>
Protein_chain_A 3<br>
<br>
=====================<br>
<br>
error:-<br>
<br>
<br>
Ignoring obsolete mdp entry 'title'<br>
<br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#<br>
Generated 23220 of the 23220 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 1<br>
Generated 20092 of the 23220 1-4 parameter combinations<br>
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'<br>
<br>
------------------------------<u></u>-------------------------<br>
Program grompp, VERSION 4.5.4<br>
Source code file: toppush.c, line: 1987<br>
<br>
Fatal error:<br>
No such moleculetype LIG<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors</a><br>
------------------------------<u></u>-------------------------<br>
</blockquote>
<br></div>
You have to make an attempt to solve your own problems :-) We have better things to do than oversee every move you make. Follow that link and read about this issue.<div><div></div><div><br>
<br>
Mark<br>
-- <br>
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</div></div></blockquote></div><br><br clear="all"><br></div></div><div><div></div><div class="h5">-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>
Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>