3DNA Forum

Questions and answers => MD simulations => Topic started by: shynomat on April 29, 2012, 07:49:24 pm

Title: No matching entry in atomlist.dat
Post by: shynomat on April 29, 2012, 07:49:24 pm: Dear all,

I am trying to use find_pair as shown below:
find_pair -c+ sel.pdb new.inp
I am getting this error: no matching entry for atom name [ OW] (..OW) in 'atomlist.dat'
now it is set as 'XX'
In my pdb file water is listed as OW. In this case should I add this as a new atom to atomlist.dat?
For the same analysis, I had to modify baselist.dat. The following bases were added:
DG3- 3 terminal guanine
DC5- 5 terminal cytosine

thanks
Shyno
Title: Re: No matching entry in atomlist.dat
Post by: xiangjun on April 29, 2012, 08:23:33 pm: In the default 'atomlist.dat' file, there is an entry, [.OW. O]. Presumably, yours should be added as: [..OW O].

DG3 and DC5 have already been included in 'baselist.dat' (as 'g' and 'c' respectively). What specific message does 'find_pair' output for your structure? Did you know that, as of 3DNA v2.1, you do not have to modify 'baselist.dat'? Nevertheless, it is a good idea to be explicit about each mapping.

Attaching a sample PDB file would clarify the issues.

Xiang-Jun
Title: Re: No matching entry in atomlist.dat
Post by: shynomat on May 02, 2012, 01:42:02 pm: Hello Xiangjun,

thank you very much for your reply.
You are correct, I don't need to modify the baselist.dat, actually I got that message with v 1.5 which I tried first. Now I am using v2.1beta.
Regarding the "No matching entry in atomlist.dat", my pdb format was wrong! Once I fixed that issue, everything seems fine.
thanks again for your reply and sorry for the delay in replying.

Regards
Shyno