Hi 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.
I created the pdb file (below) using Charmm for the sequence ACE-ALA-ALA-CT3. pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and CT3. Does someone have the appropriate definitions for these residues ? ( I have tried http://swissparam.ch/ 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. ) I am using GMX4.5.4. Thanks Sandeep -- Post Doc Wales Research Group Department of Chemistry Cambridge ============================================================= REMARK Charmm commands: REMARK ! CONSTRUCT STRUCTURE FROM SEQUENCE REMARK READ SEQUence CARD REMARK * REMARK 1 REMARK ALA ALA REMARK GENErate DIALA FIRSt ACE LAST CT3 WARN SETUp REMARK ATOM 1 CAY ALA 1 -2.160 0.537 0.930 1.00 0.00 DIAL ATOM 2 HY1 ALA 1 -2.466 0.003 0.005 1.00 0.00 DIAL ATOM 3 HY2 ALA 1 -2.562 1.572 0.910 1.00 0.00 DIAL ATOM 4 HY3 ALA 1 -2.562 0.001 1.816 1.00 0.00 DIAL ATOM 5 CY ALA 1 -0.672 0.582 1.009 1.00 0.00 DIAL ATOM 6 OY ALA 1 -0.105 1.128 1.954 1.00 0.00 DIAL ATOM 7 N ALA 1 0.000 0.000 0.000 1.00 0.00 DIAL ATOM 8 HN ALA 1 -0.453 -0.444 -0.769 1.00 0.00 DIAL ATOM 9 CA ALA 1 1.459 0.000 0.000 1.00 0.00 DIAL ATOM 10 HA ALA 1 1.812 -0.497 0.897 1.00 0.00 DIAL ATOM 11 CB ALA 1 1.949 -0.834 -1.207 1.00 0.00 DIAL ATOM 12 HB1 ALA 1 1.514 -1.854 -1.155 1.00 0.00 DIAL ATOM 13 HB2 ALA 1 1.628 -0.373 -2.167 1.00 0.00 DIAL ATOM 14 HB3 ALA 1 3.056 -0.932 -1.214 1.00 0.00 DIAL ATOM 15 C ALA 1 2.096 1.401 0.000 1.00 0.00 DIAL ATOM 16 O ALA 1 1.425 2.432 0.000 1.00 0.00 DIAL ATOM 17 N ALA 2 3.451 1.458 0.000 1.00 0.00 DIAL ATOM 18 HN ALA 2 3.954 0.594 0.000 1.00 0.00 DIAL ATOM 19 CA ALA 2 4.276 2.664 0.000 1.00 0.00 DIAL ATOM 20 HA ALA 2 4.065 3.236 -0.897 1.00 0.00 DIAL ATOM 21 CB ALA 2 3.864 3.539 1.207 1.00 0.00 DIAL ATOM 22 HB1 ALA 2 2.776 3.756 1.155 1.00 0.00 DIAL ATOM 23 HB2 ALA 2 4.063 3.014 2.167 1.00 0.00 DIAL ATOM 24 HB3 ALA 2 4.407 4.508 1.214 1.00 0.00 DIAL ATOM 25 C ALA 2 5.791 2.399 0.000 1.00 0.00 DIAL ATOM 26 O ALA 2 6.597 3.328 0.000 1.00 0.00 DIAL ATOM 27 NT ALA 2 6.175 1.110 0.000 1.00 0.00 DIAL ATOM 28 HNT ALA 2 5.528 0.351 0.000 1.00 0.00 DIAL ATOM 29 CAT ALA 2 7.566 0.777 0.000 1.00 0.00 DIAL ATOM 30 HT1 ALA 2 8.048 1.201 0.907 1.00 0.00 DIAL ATOM 31 HT2 ALA 2 7.683 -0.327 0.000 1.00 0.00 DIAL ATOM 32 HT3 ALA 2 8.048 1.201 -0.907 1.00 0.00 DIAL TER 33 ALA 2 END
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
