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* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
> <mailto: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> 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.
[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> http://folding.bmc.uu.se
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