[gmx-users] pdb2gmx not recognizing disulfides

[Yang Ye]

If you are using trjconv, a gro or pdb can be fed to -s option. tpr is 
not necessary.

Regards,
Yang Ye

On 7/2/2007 10:01 PM, Russell Green wrote:
> Hmm...well the thing is, I just need a .tpr file (which I was getting 
> with pdb2gmx followed by grompp) so I can convert an amber pdb 
> trajectory to xtc format. The simulation is already complete, I'm just 
> converting it, but of course the atoms from the tpr need to match 
> those of the trajectory. So should I still be doing something 
> different other than my idea to change the residue names of the .itp 
> files, as mentioned previously? Sorry for some of my ignorance, I'm 
> still new with much of this. Thanks for all the suggestions and input!
>  
> Thanks,
> Russell Green
>
>  
> On 7/2/07, *David van der Spoel* <spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>     Russell Green wrote:
>     >
>     >    I did try changing the bond length but it wouldn't catch all the
>     > disulfides. I do have multiple chains but I don't believe they
>     should be
>     > merged. My current work around is to just leave the disulfide
>     residues
>     > named CYX according to the amber format and then change them to
>     CYS2 in
>     > the .itp files for the corresponding .top file. This way pdb2gmx
>     doesn't
>     > protonate the disulfide residues and the charges for CYS2 are
>     > maintained. If anyone thinks this is not a good idea, please
>     tell me.
>     >
>     it's still not clear what you want to do. if your CYS are at 0.2 nm
>     distance pdb2gmx will make the bonds. if they are not, why would you
>     want them to form? anyway, if you want to do that, please follow
>     Tsjerk's advice below.
>
>
>     > Thanks,
>     > Russell
>     >
>     > On 7/2/07, *Tsjerk Wassenaar* <tsjerkw at gmail.com
>     <mailto:tsjerkw at gmail.com>
>     > <mailto: tsjerkw at gmail.com <mailto:tsjerkw at gmail.com>>> wrote:
>     >
>     >     Hi Russel,
>     >
>     >     You never mentioned the distance between the
>     >     'sulphurs-that-wouldn't-connect'. Are they beyond the range
>     normal for
>     >     disulphide bonds? If so, you could try to add an additional
>     entry in
>     >     the specbond.dat file with a different bond length. Maybe
>     you'll have
>     >     to change the residue name first, although it could work
>     without (I
>     >     don't know whether pdb2gmx properly handles multiple multiple
>     >     distances for the same atom pair, but it's easy to find out).
>     >     Another thing you never mentioned is whether the cysteines
>     are from
>     >     one chain or from different chains. In the latter case, you
>     have to
>     >     use the option -merge with pdb2gmx. pdb2gmx will not usually
>     make
>     >     bonds between different chains.
>     >
>     >
>
>     --
>     David van der Spoel, Ph.D.
>     Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
>     University.
>     Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax:
>     +4618511755.
>     spoel at xray.bmc.uu.se
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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