[gmx-users] pds files without bond information
erikm at xray.bmc.uu.se
Thu Feb 21 11:21:57 CET 2013
On Feb 20, 2013, at 9:58 PM, Erik Marklund wrote:
> pdb2gmx generate the connectivity from the residue and atom
> sequences (the file format specs state the order in which they
> appear) and the distances between atoms. This is fairly robust as
> long as the coordinates aren't unusually bad. For instance, if two
> carbons are located at ~1 C-C bond length they are very likely to be
> bound to each other.
... with the help of the information in the rtp files of course. As
Justin pointed out.
> On Feb 20, 2013, at 7:59 PM, cdo wrote:
>> Hi all,
>> I'm new to Gromacs with a very basic question while I was reading
>> Tried to search this but I couldn't narrow down to useful
>> discussions so
>> It's simple. I saw some pdb files in the Tutorias. (such as
>> LYSOZYME). But
>> this particular pdb file do not have all the connectivity
>> information. But
>> still seems to work well in creating topology files. How is this
>> Don't I have to have all the connectivity information correctly in
>> pdb file
>> to start with? What is the minimum requirement for the pdb file to
>> be used
>> in Gromacs?
>> Does pdb2gmx generate bondtype and atom type information correctly
>> without some connectivity information in the pdb file? How
>> information about the structure of molecules should I have in order
>> correctly generate input files for Gromacs?
>> Thank you,
>> View this message in context: http://gromacs.5086.n6.nabble.com/pds-files-without-bond-information-tp5005737.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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