---------- Forwarded message ---------- From: Sepideh Soltani <[email protected]> Date: Thu, Apr 8, 2010 at 12:33 AM Subject: Fwd: moleculetype CU1+ is redefined To: [email protected]
Begin forwarded message: *From: *Sepideh Soltani <[email protected]> *Date: *April 8, 2010 12:33:00 AM EDT *To: *[email protected] *Subject: **moleculetype CU1+ is redefined* I am running with gromacs 4.0.5. I am trying to do gromacs tutorial for drug-enzyme complex. I did this tutorial step by step but when I used the grompp step befor the energy minimization "grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr" I found the following error: ------------------------------------------------------- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 947 Fatal error: Atomtype CB not found ------------------------------------------------------- then I found this your answer in mailing list : The PRODRG server generates topologies for the gmx force field (ffgmx; deprecated!). You most likely want to have a topology compliant with the Gromos96 force fields (e.g. ffG43a2). For this you need to use the beta version of the PRODRG server. and finally I used Beta version of the PRODRG and used DRGAPH.GRO instead of DRGFIN.GRO becase I had another problem: ------------------------------------------------------- Program grompp, VERSION 4.0.5 Source code file: grompp.c, line: 362 Fatal error: number of coordinates in coordinate file (trp_b4ion.gro, 14622) does not match topology (trp.top, 14612) ------------------------------------------------------- But now when again I used the grompp step befor the energy minimization ("grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr" ) I have this problem: ------------------------------------------------------- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1006 Fatal error: moleculetype CU1+ is redefined ------------------------------------------------------- Now I don't know Is this change correct? If yes, How can I solve this new problem. If not How can I solve previous problem. Thank you for your help, Hanna
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