[gmx-users] No default U-B types in CHARMM36 FF

[Albert]

thank you for kind comments.

I checked that all residues are in the same chain X. I add NMA as 
Protein in residuetypes.dat file and run pdb2gmx command again, it still 
have some problems:

Linking CYS-121 SG-638 and CYS-198 SG-1229...
Select start terminus type for ACE-35
  0: NH3+
  1: NH2
  2: 5TER
  3: None
3
Start terminus ACE-35: None
Select end terminus type for NMA-339
  0: COO-
  1: COOH
  2: CT2
  3: 3TER
  4: None
3
End terminus NMA-339: 3TER

-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.5
Source code file: /home/albert/gromacs-4.6.5/src/kernel/pdb2top.c, line: 
1148

Fatal error:
atom O3' not found in buiding block 305NMA while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Art For Arts Sake, Money For Gods Sake" (10 CC)



I don't understand why it need O3 for NMA. Here are coordinates for my 
NMA residue:
ATOM   2363  N   NMA X 339      51.520  10.650  31.420  0.00 
0.00           N
ATOM   2364  CH3 NMA X 339      51.540   9.620  30.390  0.00 
0.00           C


here are information from merge.rtp file:
[ NMA ] ; terminal residue, provided by Mark Abraham
  [ atoms ]
        N       NH1     -0.470  1
        H       H       0.310   1
        CH3     CT3     -0.110  1
        HH31    HA3     0.090   1
        HH32    HA3     0.090   1
        HH33    HA3     0.090   1


both file doesn't have O3 atoms....

thanks a lot






On 04/13/2014 05:20 PM, Justin Lemkul wrote:
> Scroll up in the pdb2gmx screen output.  When it breaks down the 
> chains, it will show you what is considered "Protein" and what is 
> considered "Other."  The residue "NMA" does not appear anywhere in 
> residuetypes.dat, so pdb2gmx decides that you have a "Protein" chain 
> from ACE-1 to GLY-338, and then something else to deal with 
> separately.  Add NMA to residuetypes.dat as a Protein type and it will 
> work.