priyanka srivastava wrote:
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.
this means the angle can be anything. you have to add the force constant
and reference angle from a similar one in the rtp file (and run pdb2gmx
again) or in your top file.
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
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