leila karami wrote:
Hi
I used amber03 force field in gromacs to study pr-dna interaction.
I compare my pdb file and ffamber03.rtp file.
I should correct my pdb file to tally with rtp file. N-terminal (NUMBER
1) and C-terminal (NUMBER 70) of my protein is GLY.
pdb file and rtp file relating to gly1 and gly70 are placed in follow.
pdb file of gly1:
1 N NGLY 1
2 CA NGLY 1
3 C NGLY 1
4 O NGLY 1
5 1H NGLY 1
6 2HA NGLY 1
7 2H NGLY 1
8 3H NGLY 1
9 1HA NGLY 1
rtp file of gly1:
[ NGLY ]
[ atoms ]
N amber99_39 0.29430 1
H1 amber99_17 0.16420 2
H2 amber99_17 0.16420 3
H3 amber99_17 0.16420 4
CA amber99_11 -0.01000 5
HA1 amber99_28 0.08950 6
HA2 amber99_28 0.08950 7
C amber99_2 0.61630 8
O amber99_41 -0.57220 9
pdb file of gly70:
1 N CGLY A 70
2 CA CGLY A 70
3 C CGLY A 70
4 O CGLY A 70
5 H CGLY A 70
6 2HA CGLY A 70
7 1HA CGLY A 70
8 OXT CGLY A 70
9 CGLY A 70
rtp file of gly70:
[ CGLY ]
[ atoms ]
N amber99_34 -0.38210 1
H amber99_17 0.26810 2
CA amber99_11 -0.24930 3
HA1 amber99_19 0.10560 4
HA2 amber99_19 0.10560 5
C amber99_2 0.72310 6
OC1 amber99_45 -0.78550 7
OC2 amber99_45 -0.78550 8
before correction of pdb file, following warning and error was came up:
*WARNING: atom H is missing in residue GLY 1 in the pdb file
You might need to add atom H to the hydrogen database of
residue GLY
in the file ff???.hdb (see the manual)
*
*Fatal error:
There were 1 missing atoms in molecule Protein_A, if you want to use
this incomplete topology anyhow, use the option -missing
*
ffamber03.hdb:
* *
I don't understand what you're doing. There is no GLY 1 in the above.
Please describe the contents of your .pdb file and give your pdb2gmx
command line.
Mark
NGLY 2
3 4 H N CA C
2 6 HA CA N C
I didn't use -missing option.
please guide me.
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