[gmx-users] about rtp and pdb
David
spoel at xray.bmc.uu.se
Wed Nov 20 07:38:54 CET 2002
On Wed, 2002-11-20 at 08:19, 吴显辉 wrote:
> Hi, David,
> 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.
It looks good, however it is hard to specify problems just by looking at
it. How do you treat the hydrogens? Explcitly or implicitly (you have
CH3 in e.g. X topology, but hydrogens in the pdb file). You can use
pdb2gmx -ignh to get rid of the hydrogens. You do want hydrogens for
polar groups at least.
> [-X-]
> [atoms]
> C C 0.180 1
> O O -0.180 1
> CA CH2 0.000 2
> CB CH 0.000 3
> CG CH3 0.180 4
> OG OS -0.180 4
> [bonds]
> C O
> C CA
> -OG C
> CA CB
> CB CG
> CB OG
> [impropers]
> -O C O CA
> -O -CA C O
> CA CB CG OG
>
> [-OCH2CH3]
> [atoms]
> OG OS -0.180 1
> CA CH2 0.180 1
> CB CH3 0.000 2
> [bonds]
> CA CB
> CA OG
> [CH3CO-]
> [atoms]
> C C 0.180 1
> O O -0.180 1
> CA CH3 0.000 2
> [bonds]
> C O
> C CA
> -OG C
> [impropers]
> -O C O CA
> -CB OG C O
>
> Are there something wrong?
> 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.
> 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.
> HEADER
> REMARK try
> HETATM 1 C 1 0.000 0.000 0.000
> HETATM 2 C 1 0.000 0.000 1.515
> HETATM 3 O 1 -0.982 -0.013 2.214
> HETATM 4 C 1 1.449 -0.016 3.429
> HETATM 5 O 1 1.266 0.000 1.982
> HETATM 6 C 1 1.418 1.405 3.968
> HETATM 7 H 1 -1.013 0.076 -0.386
> HETATM 8 H 1 0.628 0.821 -0.359
> HETATM 9 H 1 0.484 -0.920 -0.341
> ..........................................
>
>
> Second:
> COMPND ?
> REMARK File generated by Swiss-PdbViewer 3.70b0
> REMARK http://www.expasy.org/spdbv/
> CRYST1 54.800 58.700 67.500 90.00 90.00 90.00 P 21 21 21 4
> ATOM 1 N ILE 16 35.603 19.727 20.250 1.00 13.41
> ATOM 2 CA ILE 16 35.562 20.655 19.081 1.00 13.40
> ATOM 3 C ILE 16 36.798 20.420 18.264 1.00 13.62
> ATOM 4 O ILE 16 37.907 20.471 18.784 1.00 13.71
> ATOM 5 CB ILE 16 35.547 22.145 19.535 1.00 13.12
> ATOM 6 CG1 ILE 16 34.314 22.418 20.479 1.00 14.86
> ATOM 7 CG2 ILE 16 35.560 23.085 18.292 1.00 13.33
> ATOM 8 CD1 ILE 16 32.952 22.518 19.778 1.00 13.96
> ATOM 9 N VAL 17 36.602 20.030 17.011 1.00 13.41
> ATOM 10 CA VAL 17 37.694 19.824 16.070 1.00 12.61
> ATOM 11 C VAL 17 37.835 21.083 15.227 1.00 12.59
> ATOM 12 O VAL 17 36.841 21.624 14.725 1.00 10.58
> ATOM 13 CB VAL 17 37.389 18.626 15.132 1.00 13.98
> ATOM 14 CG1 VAL 17 38.528 18.432 14.158 1.00 12.06
> ATOM 15 CG2 VAL 17 37.126 17.326 15.974 1.00 12.54
> ATOM 16 N GLY 18 39.060 21.590 15.138 1.00 12.26
> ATOM 17 CA GLY 18 39.328 22.714 14.263 1.00 14.63
> ATOM 18 C GLY 18 38.822 24.043 14.797 1.00 17.48
> ATOM 19 O GLY 18 38.541 24.963 14.023 1.00 17.10
> ATOM 20 N GLY 19 38.721 24.157 16.118 1.00 16.69
> ATOM 21 CA GLY 19 38.243 25.391 16.707 1.00 16.54
>
> ........................................
>
> Could tell me what kind of factor made me failure, rtp files format or pdb file format?
>
> Thank you very much.
>
> All your bests,
> Xianhui Wu
--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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