| Thanks Tsjerk Yes, there was a non-standard amino acid residue and it was not recognising it as part of the protein. I changed the total number of residues in the aminoacid.dat file (which I had not!) and then everything worked ok. Ashutosh On Mar 16, 2006, at 3:09 AM, Tsjerk Wassenaar wrote: Hi Ashutosh,
If no index file is explicitly given to grompp, it will use default index group (as if you did echo q | make_ndx -f test_b4pr.gro -o index.ndx) Grompp does not know of definitions given in the .top file with regards to the groups. Does your protein contain some non-standard residues? Try to explicitly create an index file and see if the groups "Protein" and "SOL" cover all atoms in your system. ( N(Proteins) + N(SOL) = N(System) ). If not, make adjustments to the index file by merging appropriate groups, i.e. merge non-standard protein groups with the protein if necessary. Note that this basically was the problem given in the last post about "Not enough ref_t and tau_t values".
Cheers,
Tsjerk
On 3/16/06, X.Periole <[EMAIL PROTECTED]> wrote: On Wed, 15 Mar 2006 17:21:52 -0600
Ashutosh Jogalekar <[EMAIL PROTECTED]> wrote:
> I know this question has been discussed a number of
>times on the list, but almost everytime it has been
>discussed in reference to the index file.
> I am getting this error during grompp for the position
>restrained MD even though I am not using any index file.
>The only groups I have are solvent and protein and
>accordingly, there are two columns for these two in the
>tau_t and ref_t fields in the pr.mdp file:
>
> tau_t= 0.1 0.1
> tc_grps= protein sol
> ref_t= 300 300
>
> my command is:
>
> grompp -f pr.mdp -c test_b4pr.gro -p test.top -o
>test_em.tpr
>
> In spite of this, the error is showing up again and
>again. The top file also has a row only for protein and
>solvent.
If all the atoms of your protein or solvent are not
included
in the indexes defined by default (protein sol) I think
grompp find them out of any index and then looks for more
tau_t and ref_t ... I would check the topology of your
system. It might be uncorrect.
XAvier
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
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
--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
_______________________________________________ Please don't post (un)subscribe requests to the list. Use the |
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
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
