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On 21/06/2011 4:33 PM, bharat gupta wrote:
<blockquote
cite="mid:BANLkTimW3Q3UwS5rH5d7O2WViYKTmdpbrg@mail.gmail.com"
type="cite">So, after adding 1 NA ion, I started with energy
mimization, but I am getting the following error after md run
command :-<br>
</blockquote>
<br>
Please search for help first.<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings">http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTimW3Q3UwS5rH5d7O2WViYKTmdpbrg@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
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 class="h5"><br>
<br>
<br>
<div class="gmail_quote">On Tue, Jun 21, 2011 at 2:13 PM,
Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>On 21/06/2011 3:03 PM, bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt
0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
204, 204); 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>
-------------------------------------------------------<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 moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors"
target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<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><br>
<br>
Mark<br>
-- <br>
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</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
</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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div>
<br>
</blockquote>
<br>
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