Dear justin here it is. creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6# WARNING 1 [file em.mdp, line unknown]: Unknown left-hand 'constrains' in parameter file WARNING 2 [file em.mdp, line unknown]: Unknown left-hand 'nslist' in parameter file checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Cleaning up temporary file gromppYyltp4 ------------------------------------------------------- Program grompp, VERSION 3.3.2 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'C' not found! ------------------------------------------------------- "That Was Pretty Cool" (Beavis) and tfe.pdb is : REMARK 888 REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC) MODEL 1 HETATM 1 C1 UNK 1 -0.080 1.504 0.000 1.00 0.00 C HETATM 2 C2 UNK 1 0.741 0.249 0.000 1.00 0.00 C HETATM 3 O1 UNK 1 0.380 1.963 0.000 1.00 0.00 O HETATM 4 F1 UNK 1 -0.096 -0.849 0.000 1.00 0.00 F HETATM 5 F2 UNK 1 1.537 0.219 -1.127 1.00 0.00 F HETATM 6 F3 UNK 1 1.537 0.219 1.127 1.00 0.00 F HETATM 7 H1 UNK 1 -0.031 2.830 0.000 1.00 0.00 H CONECT 1 2 3 CONECT 2 1 4 5 6 CONECT 3 1 7 CONECT 7 3 CONECT 4 2 CONECT 5 2 CONECT 6 2 ENDMDL and topology is ; PEPTIDE A5 OR AUREIN 1.2 ; ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetype ] ; Name nrexcl Protein_A 3 [ atoms ] \\\ ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "spce.itp" ; Include tfe topology #include "tfe.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name PEPTIDE A5 OR AUREIN 1.2 in water [ molecules ] ; Compound #mols Protein_A 1 SOL 1308 TFE 40 --again thanks . sh-karbalaee _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
