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<P><FONT color=#ffffff>Hi, David,</FONT></P>
<P><FONT color=#ffffff> I have already created rtp file manaul.
Would you please check it for me,it's the first time I ever created rtp files.My
polymer is CH3CO-Xn-OCH2CH3.I have created three rtp files.One is CH3CO-, the
other is -X- residue,the last is -OCH2CH3.</FONT></P>
<P><FONT color=#ffffff>[-X-]<BR> [atoms]<BR>
C C
0.180 1<BR> O
O -0.180 1<BR>
CA CH2 0.000 2<BR>
CB CH 0.000
3<BR> CG CH3 0.180
4<BR> OG OS -0.180
4</FONT></P>
<P><FONT color=#ffffff> [bonds]<BR> C
O<BR> C CA<BR> -OG
C<BR> CA CB<BR> CB CG<BR>
CB OG<BR> [impropers]<BR> -O
C O CA<BR> -O -CA
C O<BR> CA CB CG
OG<BR> <BR>[-OCH2CH3]<BR> [atoms]<BR> OG
OS -0.180 1<BR> CA
CH2 0.180 1<BR> CB
CH3 0.000 2</FONT></P>
<P><FONT color=#ffffff> [bonds]<BR> CA CB<BR>
CA OG</FONT></P>
<P><FONT color=#ffffff>[CH3CO-]<BR> [atoms] <BR> C
C 0.180 1<BR>
O O
-0.180 1<BR> CA CH3
0.000 2</FONT></P>
<P><FONT color=#ffffff> [bonds]<BR> C
O<BR> C CA<BR> -OG
C</FONT></P>
<P><FONT color=#ffffff> [impropers]<BR> -O
C O CA<BR> -CB
OG C O</FONT></P>
<P> </P>
<P><FONT color=#ffffff>Are there something wrong?</FONT></P>
<P><FONT color=#ffffff>After I finished creating rtp files,I have
tried to use pdb2gmx to transfer pdb file to top and gro files.There are
something wrong too. I hope it is not reason of wrong rtp files.</FONT></P>
<P><FONT color=#ffffff> The data of polymer is from ab initio
calculation.Its pdb format is different from pdb file download from Protein Data
Bank (Brookhaven National Labratory).I will show you two pieces of file
respectively. First piece of file is from ab initio or Chem3D. The second piece
of file is from Protein Data Bank.</FONT></P>
<P>HEADER<BR>REMARK try<BR>HETATM 1
C
1 0.000 0.000
0.000<BR>HETATM 2
C
1 0.000 0.000
1.515<BR>HETATM 3
O
1 -0.982 -0.013
2.214<BR>HETATM 4
C
1 1.449 -0.016
3.429<BR>HETATM 5
O
1 1.266 0.000
1.982<BR>HETATM 6
C
1 1.418 1.405
3.968<BR>HETATM 7
H
1 -1.013 0.076
-0.386<BR>HETATM 8
H
1 0.628 0.821
-0.359<BR>HETATM 9
H
1 0.484 -0.920 -0.341</P>
<P>..........................................</P>
<P> </P>
<P> </P>
<P>Second:</P>
<P>COMPND ?<BR>REMARK File generated by
Swiss-PdbViewer 3.70b0<BR>REMARK <A
href="http://www.expasy.org/spdbv/">http://www.expasy.org/spdbv/</A><BR>CRYST1
54.800 58.700 67.500 90.00 90.00 90.00
P 21 21 21 4
<BR>ATOM 1 N
ILE 16 35.603 19.727
20.250 1.00 13.41<BR>ATOM 2 CA
ILE 16 35.562 20.655
19.081 1.00 13.40<BR>ATOM 3
C ILE 16
36.798 20.420 18.264 1.00
13.62<BR>ATOM 4 O
ILE 16 37.907 20.471
18.784 1.00 13.71<BR>ATOM 5 CB
ILE 16 35.547 22.145
19.535 1.00 13.12<BR>ATOM 6 CG1
ILE 16 34.314 22.418
20.479 1.00 14.86<BR>ATOM 7 CG2
ILE 16 35.560 23.085
18.292 1.00 13.33<BR>ATOM 8 CD1
ILE 16 32.952 22.518
19.778 1.00 13.96<BR>ATOM 9
N VAL 17
36.602 20.030 17.011 1.00
13.41<BR>ATOM 10 CA VAL
17 37.694 19.824 16.070 1.00
12.61<BR>ATOM 11 C
VAL 17 37.835 21.083
15.227 1.00 12.59<BR>ATOM 12 O
VAL 17 36.841 21.624
14.725 1.00 10.58<BR>ATOM 13 CB
VAL 17 37.389 18.626
15.132 1.00 13.98<BR>ATOM 14 CG1
VAL 17 38.528 18.432
14.158 1.00 12.06<BR>ATOM 15 CG2
VAL 17 37.126 17.326
15.974 1.00 12.54<BR>ATOM 16 N
GLY 18 39.060 21.590
15.138 1.00 12.26<BR>ATOM 17 CA
GLY 18 39.328 22.714
14.263 1.00 14.63<BR>ATOM 18 C
GLY 18 38.822 24.043
14.797 1.00 17.48<BR>ATOM 19 O
GLY 18 38.541 24.963
14.023 1.00 17.10<BR>ATOM 20 N
GLY 19 38.721 24.157
16.118 1.00 16.69<BR>ATOM 21 CA
GLY 19 38.243 25.391
16.707 1.00 16.54<BR></P>
<P>........................................</P>
<P> </P>
<P>Could tell me what kind of factor made me failure, rtp files format or pdb
file format? </P>
<P> </P>
<P>Thank you very much.</P>
<P> </P>
<P>All your bests,</P>
<P>Xianhui Wu</P>
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