Dear Justin
Many thanks for this...all is now well.
Best
Garry
On 24 Oct 2008, at 20:42, Justin A. Lemkul wrote:
Wouldn't it be better to couple the Protein and Zn2+ together (i.e.,
index group Protein_Zn2+)? Coupling ions separately often leads to
weird behavior/explosions when they're free in the solvent. I've
never dealt with proteins that have ions bound, so I'm curious to
see what everyone else thinks about this, just as a point of
curiosity.
-Justin
Andy Shelley wrote:
Garry,
I believe you are trying to not temperature couple the 4 zincs. To
do this put the 4 zincs in one group and include that group in the
listing of tc_grps and then correspondingly assign tau_t. tau_t=0
means no temperature coupling, but I think you will also need to
give a temperature for the tau_t=0 even though that group does not
have temperature coupling. See section 7.3.13 in the gromacs user
manual.
Andy
garry wrote:
>
> I am a novice at Gromacs (although I used Gromos 20+ years
ago!)....I
> have a dimer with two zincs per monomer, and I get the following
> complaint when running the grompp with pr.dmp, which I assume is
> referring to the 4 zincs.
>
>
> There are: 6789 OTHER residues
> There are: 262 PROTEIN residues
> There are: 0 DNA residues
> Analysing Protein...
> Analysing Other...
>
> ------------------------------
-------------------------
> Program grompp, VERSION 3.3.2
> Source code file: readir.c, line: 865
>
> Fatal error:
> 4 atoms are not part of any of the T-Coupling groups
> -------------------------------------------------------
>
> the zincs are in the pdb file as (properly formatted in the pdb
file!):
>
> ATOM 2103 SG CYS B 133 -10.574 -5.438 18.502 1.00
> 51.42 S
> ATOM 2104 C CYS B 133 -10.084 -9.287 20.134 1.00
> 50.50 C
> ATOM 2105 O CYS B 133 -9.171 -9.545 20.923 1.00
> 50.69 O
> HETATM 2106 ZN ZN2+C 1 -12.350 1.941 1.066 1.00
> 43.80 ZN
> HETATM 2107 ZN ZN2+C 2 -21.690 2.493 -3.958 1.00
> 38.99 ZN
> HETATM 2109 ZN ZN2+C 3 -11.783 11.509 10.159 1.00
> 28.52 ZN
> HETATM 2108 ZN ZN2+C 4 -17.911 8.618 18.155 1.00
> 32.42 ZN
>
> What am I doing wrong ?
>
What does your .mdp file look like? Have you included the Zn2+
within one of
your tc-grps?
-Justin
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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 [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
