Hi <div><br></div><div>I am trying to set up a simulation for dialanine using charmm27 ff but am getting errors in pdb2gmx due to missing definitions in rtp file. </div><div><br></div><div>I created the pdb file (below) using Charmm for the sequence ACE-ALA-ALA-CT3. </div>
<div><br></div><div>pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and CT3. </div><div><br></div><div>Does someone have the appropriate definitions for these residues ? </div><div>( I have tried <a href="http://swissparam.ch/">http://swissparam.ch/</a> to generate an itp file for the molecule, but upon using it in GMX it does not give the same energy as that from charmm. ) </div>
<div><br></div><div>I am using GMX4.5.4. </div><div><br></div><div>Thanks</div><div>Sandeep </div><div><br></div><div>
--</div><div>Post Doc </div><div>Wales Research Group </div><div>Department of Chemistry </div><div>Cambridge </div><div><br></div><div>=============================================================</div><div>REMARK Charmm commands: </div>
<div><div>REMARK ! CONSTRUCT STRUCTURE FROM SEQUENCE </div><div>REMARK READ SEQUence CARD</div><div>
REMARK *</div><div>REMARK 1</div><div>REMARK ALA ALA </div><div>
REMARK GENErate DIALA FIRSt ACE LAST CT3 WARN SETUp</div></div><div><div>REMARK </div><div>ATOM 1 CAY ALA 1 -2.160 0.537 0.930 1.00 0.00 DIAL</div><div>ATOM 2 HY1 ALA 1 -2.466 0.003 0.005 1.00 0.00 DIAL</div>
<div>ATOM 3 HY2 ALA 1 -2.562 1.572 0.910 1.00 0.00 DIAL</div><div>ATOM 4 HY3 ALA 1 -2.562 0.001 1.816 1.00 0.00 DIAL</div><div>ATOM 5 CY ALA 1 -0.672 0.582 1.009 1.00 0.00 DIAL</div>
<div>ATOM 6 OY ALA 1 -0.105 1.128 1.954 1.00 0.00 DIAL</div><div>ATOM 7 N ALA 1 0.000 0.000 0.000 1.00 0.00 DIAL</div><div>ATOM 8 HN ALA 1 -0.453 -0.444 -0.769 1.00 0.00 DIAL</div>
<div>ATOM 9 CA ALA 1 1.459 0.000 0.000 1.00 0.00 DIAL</div><div>ATOM 10 HA ALA 1 1.812 -0.497 0.897 1.00 0.00 DIAL</div><div>ATOM 11 CB ALA 1 1.949 -0.834 -1.207 1.00 0.00 DIAL</div>
<div>ATOM 12 HB1 ALA 1 1.514 -1.854 -1.155 1.00 0.00 DIAL</div><div>ATOM 13 HB2 ALA 1 1.628 -0.373 -2.167 1.00 0.00 DIAL</div><div>ATOM 14 HB3 ALA 1 3.056 -0.932 -1.214 1.00 0.00 DIAL</div>
<div>ATOM 15 C ALA 1 2.096 1.401 0.000 1.00 0.00 DIAL</div><div>ATOM 16 O ALA 1 1.425 2.432 0.000 1.00 0.00 DIAL</div><div>ATOM 17 N ALA 2 3.451 1.458 0.000 1.00 0.00 DIAL</div>
<div>ATOM 18 HN ALA 2 3.954 0.594 0.000 1.00 0.00 DIAL</div><div>ATOM 19 CA ALA 2 4.276 2.664 0.000 1.00 0.00 DIAL</div><div>ATOM 20 HA ALA 2 4.065 3.236 -0.897 1.00 0.00 DIAL</div>
<div>ATOM 21 CB ALA 2 3.864 3.539 1.207 1.00 0.00 DIAL</div><div>ATOM 22 HB1 ALA 2 2.776 3.756 1.155 1.00 0.00 DIAL</div><div>ATOM 23 HB2 ALA 2 4.063 3.014 2.167 1.00 0.00 DIAL</div>
<div>ATOM 24 HB3 ALA 2 4.407 4.508 1.214 1.00 0.00 DIAL</div><div>ATOM 25 C ALA 2 5.791 2.399 0.000 1.00 0.00 DIAL</div><div>ATOM 26 O ALA 2 6.597 3.328 0.000 1.00 0.00 DIAL</div>
<div>ATOM 27 NT ALA 2 6.175 1.110 0.000 1.00 0.00 DIAL</div><div>ATOM 28 HNT ALA 2 5.528 0.351 0.000 1.00 0.00 DIAL</div><div>ATOM 29 CAT ALA 2 7.566 0.777 0.000 1.00 0.00 DIAL</div>
<div>ATOM 30 HT1 ALA 2 8.048 1.201 0.907 1.00 0.00 DIAL</div><div>ATOM 31 HT2 ALA 2 7.683 -0.327 0.000 1.00 0.00 DIAL</div><div>ATOM 32 HT3 ALA 2 8.048 1.201 -0.907 1.00 0.00 DIAL</div>
<div>TER 33 ALA 2</div><div>END</div></div><div><br></div>