Joern Lenz wrote:
dear users,
i am simulating a complex of DNA and protein.
also i looked through the mailing list I did not find any solution to my
problem.
i am using make_ndx with:
make_ndx -f blah_ion -o blah_ion
and in my mdp file i use:
tcoupl = berendsen
tau_t = 0.1 0.1 0.1 0.1 0.1 1.0 0.5 0.5 0.5 0.5
tc_grps = Protein SOL LYP HIP CYN NA+ DG DA DC DT
ref_t = 300 300 300 300 300 300 300 300 300 300
make_ndx then asks me to choose of:
0 System : 317421 atoms
1 Protein : 6937 atoms
2 Protein-H : 3465 atoms
3 C-alpha : 445 atoms
4 Backbone : 1335 atoms
5 MainChain : 1780 atoms
6 MainChain+Cb : 2193 atoms
7 MainChain+H : 2205 atoms
8 SideChain : 4732 atoms
9 SideChain-H : 1685 atoms
10 Prot-Masses : 6937 atoms
11 Non-Protein : 310484 atoms
12 LYP : 528 atoms
13 HIP : 234 atoms
14 CYN : 11 atoms
15 DA : 192 atoms
16 DG : 495 atoms
17 DT : 192 atoms
18 DC : 450 atoms
19 SOL : 308340 atoms
20 Na+ : 42 atoms
21 Other : 310484 atoms
and i take the numbers: 1, 12, 13, 14, 15, 16, 17, 18, 19 and 20
I think I with this selection I have no atom twice (otherwise there would be
complaining of make_ndx) and covered all atoms in my system.
I looked through the top and pdb files and did not see any residues that are
not mentiond in the table above.
=>> the same error occurs if i choose number 0 from the table above also -
from my point of view this should cover all atoms at once, shouldn't it ?
Nevertheless I got the following error:
Fatal error:
126 atoms are not part of any of the T-Coupling groups
Do you have any suggestions or do I not see the wood for the trees any more ?
Thank you so much in advance
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you probably should start by putting the file aminoacids.dat from Amber
in your directory and make a new index file. then check the mailinglist
for advise on how may charge groups you want to use.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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