On Thu, Dec 2, 2010 at 5:58 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > mohsen ramezanpour wrote: > >> Dear Tsjerk >> >> some information exist in pdb file which are not peresent in pqr and vise >> versa. >> I want to convert them to eachother in a way to conclude one's information >> to the other file. >> as you know a typical pdb file has a definite colomns and each of them >> present a definite charachter(for example charge,X-coordinate,...) >> > > Charges are not typically in .pdb files, and they certainly don't precede > the x-coordinate. Ok.I agree with you > > > my pqr has more atoms than original pdb,but It dosen't have any >> coordinates. >> > > Then it sounds like you have a useless .pqr file. The format of a proper > .pqr file is identical to that of a .pdb file, except that in place of > B-factor and occupancy fields, the charge and radius are given. Thus, what > Tsjerk told you should work, but perhaps you have a mangled input file that > makes this impossible. > Ok.I will try to produce another .pqr file again.I think both are you are right ,it seems to me my file is useless. Thanks > > -Justin > > besides converting as you said dosen't solve the problem,because PYMOL can >> not read this converted file.it <http://file.it> needs a file who has >> included atoms coordinates >> >> >> thanks in advance for your reply >> Mohsen >> >> On Thu, Nov 25, 2010 at 9:44 PM, Tsjerk Wassenaar <tsje...@gmail.com<mailto: >> tsje...@gmail.com>> wrote: >> >> Hey, >> >> For this particular conversion you can also usually use 'mv': >> >> mv file.pqr file.pdb >> >> Btw, many of these file types are human readable. It usually helps >> quite a bit to look at the files and get acquainted with the file >> formats. >> >> Cheers, >> >> Tsjerk >> >> On Nov 22, 2010 12:42 PM, "Mark Abraham" <mark.abra...@anu.edu.au >>> <mailto:mark.abra...@anu.edu.au>> wrote: >>> >>> On 22/11/2010 10:16 PM, mohsen ramezanpour wrote: > > Dear All > >>> > I had a pdb file who was incompl... >>> >>> Ask it for a pdb format. There should be no tool that builds atoms >>> that cannot write a standard file format like PDB - particularly >>> as PQR is a derivative of PDB. >>> >>> Oh, and this is a bit off-topic for this list :-) >>> >>> Mark >>> -- gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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