The only problem with my pdb file is that it has 1330 atoms, I think I cant use prodrg with more than 300.......<br>
As you pointed out, I will try to make a decent pdb file.<br>
<br>
One more question,<br>
This is a part of my .itp file<br>
<br>
295
N 40
GLU N
206 -0.28
14.0067 ; qtot -1.28<br>
296
H 40
GLU H
206
0.28 1.008 ; qtot -1<br>
297
CH1 40
GLU CA
207
0 13.019 ; qtot -1<br>
298
CH2 40
GLU CB
208
0 14.027 ; qtot -1<br>
299
CH2 40
GLU CG
209
0 14.027 ; qtot -1<br>
300
C 40
GLU CD
210 0.27
12.011 ; qtot -0.73<br>
301
OM 40 GLU
OE1 210
-0.635 15.9994 ; qtot -1.365<br>
302
OM 40 GLU
OE2 210
-0.635 15.9994 ; qtot -2<br>
303
C 40
GLU C
211 0.38
12.011 ; qtot -1.62<br>
304
O 40
GLU O
211 -0.38
15.9994 ; qtot -2<br>
<br>
while in pdb file, <br>
<br>
ATOM 295 N GLU
40 20.250 25.090 41.950
1.00 0.00<br>
ATOM 296 H GLU
40 20.340 25.930 41.420
1.00 0.00<br>
ATOM 297 CA GLU
40 20.620 25.440 43.320
1.00 0.00<br>
ATOM 298 CB GLU
40 21.210 26.840 43.440
1.00 0.00<br>
ATOM 299 CG GLU
40 22.630 26.980 42.910
1.00 0.00<br>
ATOM 300 CD GLU
40 23.050 28.450 42.940
1.00 0.00<br>
ATOM 301 OE1 GLU
40 22.680 29.310 42.130
1.00 0.00<br>
ATOM 302 OE2 GLU
40 23.780 28.750 44.050
1.00 0.00<br>
ATOM 303 HE2 GLU
40 24.010 29.710 43.890
1.00 0.00<br>
ATOM 304 C GLU
40 19.560 25.240 44.400
1.00 0.00<br>
ATOM 305 O GLU
40 19.800 24.810 45.530
1.00 0.00<br>
<br>
if you can see, HE2 is missing in .itp file, when i used pdb2gmx
program, this might be due to its description in ffgmx.rtp file which is<br>
[ GLU ]<br>
[ atoms ]<br>
N N -0.280 0<br>
H H 0.280 0<br>
CA CH1 0.000 1<br>
CB CH2 0.000 2<br>
CG CH2 0.000 3<br>
CD C 0.270 4<br>
OE1 OM -0.635 4<br>
OE2 OM -0.635 4<br>
C C 0.380 5<br>
O O -0.380 5<br>
<br>
%%%%%%%%%%%<br>
Should I add that atom type in .rtp file, or is there any other way pdb2gmx can take care of this.<br>
Thanks in advance,<br>
Vissu<br>
<br><br><div><span class="gmail_quote">On 12/21/05, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Viswanadham Sridhara wrote:<br><br>><br>> Hi Everyone,<br>> I have a .itp file, where I want to add new atoms in between, is there<br>> any way that I can add them at the end, but give the respective<br>> residue number, or should they be in order and represent .pdb file.
<br><br><br>Not easy (ch. 5). Try other means, maybe prodrg, or make a good pdb file<br>from it (if it is a protein).<br><br>> Thanks,<br>> -Vissu<br>> --<br>><br>>------------------------------------------------------------------------
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</a>.<br>><br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
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</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br>_______________________________________________<br>gmx-users mailing list
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Old Dominion University, "VIRGINIA".<br>