I'm on Blacklight.psc using Amber 12. I am going through the lipid membrane tutorial, made my lipid bi-layer in the CHARMM GUI and put the files onto blacklight.
Here's the problem:
cgaughan.tg-login1:~> charmmlipid2amber.x DOPC_pymol.pdb DOPC_128.pdb charmmlipid2amber.x Charmm Lipid Builder to AMBER Lipid 11 Convertor------------------------------------------------ v1.1 by Ross Walker (SDSC) Age Skjevik (UiB) Ben Madej (UCSD, SDSC) ------------------------------------------------ Input PDB file: DOPC_pymol.pdbOutput PDB file: DOPC_128.pdb *** STAGE 1 : STRIP REMARKS AND END STATEMENTS *** *** STAGE 2 : STRIP AND SAVE WATER *** Currently supported water: TIP3 Found TIP3 Water *** STAGE 3 : STRIP AND SAVE IONS *** Currently supported ions: CLA, POT, SOD Found Chlorine Ions Found Potassium Ions Ions were found. *** STAGE 4 : STRIP INDIVIDUAL LIPIDS TO SEPARATE FILES *** Currently supported lipids: DPPC DPPE DPPS DPPG DPPA DOPC DOPE DOPS DOPG DOPA POPC POPE POPS POPG POPA CHL1 No protein atoms detected in input pdb file. ERROR - No supported lipids found in pdb file.
So the system administrator installed the bugfix update.1: charmmlipid2amber.py:
I see that is for version 14, so I think she installed AmberTools 14 but I am using amber 12. Is that the problem?
Thanks,Chris
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Received on Thu Feb 05 2015 - 19:30:02 PST
