[gmx-users] ACE patch in FFG43a1

[priyanka srivastava]

Dear All,

I have a problem when I use ACE patch in one of my proteins using FFG43a1.

I am issuing:
pdb2gmx_3.3 -f test.pdb -ter -ignh -o test.gro

I am using -ter because I already have ACE at N terminus and NH2 at C-terminus. 

I used this test.gro and put it in a water box and went ahead with editconf and all and finally when I made the test.tpr file using grompp then it reported a warning mesg which is as follows:

warning:  [file "test.itp" , line 5010]
No default G96Angle types, using zeroes.

Now when I check the line 5010 it is:

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    1     2     3     2 
    1     2     4     2    ga_18
    3     2     4     2    ga_32

Now the first line is the line 5010 and it is nothing but the angle parameter of CH3-C-O of ACE group. As is observed here no ga_ is defined in front of line 5010. I also checked the .rtp file and there too this angle parameter is undefined. 

[ ACE ]
 [ atoms ]
    CA   CH3   0.000     0
     C     C   0.380     1
     O     O  -0.380     1
 [ bonds ]
     C    CA   gb_26
     C     O   gb_4
     C    +N   gb_9
 [ angles ]
   CA     C    +N    ga_18
    O     C    +N    ga_32
 [ impropers ]
    C    CA    +N     O    gi_1 

Although if I proceed with it then there is no problem and my simulations (production run) are running fine, but I am just curious to know why is this happening. I tried using difference force fields from pdb2gmx but all of them give me the same problem.

Another thing is, is it correct to ignore this warning message since it is for a patch only?

I shall be really thankful if I would be getting your useful suggestions on this issue.

Priyanka



      Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080807/79ad3709/attachment.html>