<p>Hi</p>
<p>I used amber03 force field in gromacs to study pr-dna interaction.<br>I compare my pdb file and ffamber03.rtp file.<br>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.<br>
pdb file and rtp file relating to gly1 and gly70 are placed in follow.</p>
<p>pdb file of gly1:</p>
<p>1 N NGLY 1<br>2 CA NGLY 1<br>3 C NGLY 1<br>4 O NGLY 1<br>5 1H NGLY 1<br>6 2HA NGLY 1<br>7 2H NGLY 1<br>8 3H NGLY 1<br>9 1HA NGLY 1</p>
<p>rtp file of gly1:</p>
<p>[ NGLY ]<br> [ atoms ]<br> N amber99_39 0.29430 1<br> H1 amber99_17 0.16420 2<br> H2 amber99_17 0.16420 3<br> H3 amber99_17 0.16420 4<br> CA amber99_11 -0.01000 5<br>
HA1 amber99_28 0.08950 6<br> HA2 amber99_28 0.08950 7<br> C amber99_2 0.61630 8<br> O amber99_41 -0.57220 9</p>
<p>pdb file of gly70:</p>
<p>1 N CGLY A 70<br>2 CA CGLY A 70<br>3 C CGLY A 70<br>4 O CGLY A 70<br>5 H CGLY A 70<br>6 2HA CGLY A 70<br>7 1HA CGLY A 70<br>8 OXT CGLY A 70<br>9 CGLY A 70</p>
<p>rtp file of gly70:</p>
<p>[ CGLY ]<br> [ atoms ]<br> N amber99_34 -0.38210 1<br> H amber99_17 0.26810 2<br> CA amber99_11 -0.24930 3<br> HA1 amber99_19 0.10560 4<br> HA2 amber99_19 0.10560 5<br>
C amber99_2 0.72310 6<br> OC1 amber99_45 -0.78550 7<br> OC2 amber99_45 -0.78550 8</p>
<div>before correction of pdb file, following warning and error was came up:</div>
<div> </div>
<div><strong>WARNING: atom H is missing in residue GLY 1 in the pdb file<br> You might need to add atom H to the hydrogen database of residue GLY<br> in the file ff???.hdb (see the manual)<br></strong></div>
<div><strong>Fatal error:<br>There were 1 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing<br></strong></div>
<div>ffamber03.hdb:</div>
<div><strong> </strong></div>
<div>NGLY 2 <br>3 4 H N CA C <br>2 6 HA CA N C </div>
<div><br>I didn't use -missing option.</div>
<p>please guide me.<br></p>