[gmx-users] pds files without bond information

[Erik Marklund]

On Feb 20, 2013, at 9:58 PM, Erik Marklund wrote:

> Hi,
>
> 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.

>
> Erik
>
> 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  
>> tutorials.
>> Tried to search this but I couldn't narrow down to useful  
>> discussions so
>> far.
>>
>> 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  
>> possible?
>>
>> 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  
>> even
>> without some connectivity information in the pdb file?    How  
>> complete
>> information about the structure of molecules should I have in order  
>> to
>> correctly generate input files for Gromacs?
>>
>> Thank you,
>> Do
>>
>>
>>
>>
>>
>>
>>
>> --
>> 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.
>> -- 
>> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> -- 
> gmx-users mailing list    gmx-users at 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 thewww  
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists