hello: Ben:
thanks for such kind helps.
It works fine for both Gromacs editconf output and CHARMM-GUI output
now.....
best
Albert
v1.1
by
Ross Walker (SDSC)
Age Skjevik (UiB)
Ben Madej (UCSD, SDSC)
------------------------------------------------
Input PDB file: gromacs.pdb
Output PDB file: new.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
Protein atoms were detected in the input pdb file.
Line count for protein section of pdb = 5145
*** STAGE 5 : CONVERT LIPID FILES TO AMBER LIPID 11 FORMAT ***
Currently supported lipids: DPPC DPPE DPPS DPPG DPPA
DOPC DOPE DOPS DOPG DOPA
POPC POPE POPS POPG POPA
CHL1
Processing: POPE
POPE Line count = 15250
POPE Lipid count = 122
Processing POPE Lipid: 1 2 3 4 5 6 7 8 9 10 11 12 13 14
15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68
69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86
87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103
104 105 106 107 108 109 110 111 112 113 114 115 116 117
118 119 120 121 122
*** STAGE 6 : COMBINE PROTEIN, LIPID, ION AND WATER FILES INTO OUTPUT
PDB ***
******* CONVERSION COMPLETE *******
On 05/08/2012 08:36 PM, Benjamin D Madej wrote:
> Hi Albert,
>
> Thanks for the bug report-- it was a problem with the ions from CHARMM. I have fixed the issue and updated the script to v1.1.1.
>
> All the best,
> Ben
> ________________________________________
> From: Albert [mailmd2011.gmail.com]
> Sent: Tuesday, May 08, 2012 2:39 AM
> To: AMBER Mailing List
> Subject: [AMBER] charmmlipid2amber.x error
>
> Hello:
>
> I am trying to convert CHARMM-GUI output into Amber12 format by command:
>
> charmmlipid2amber.x step5_assembly.pdb amber.pdb
>
> but it said:
>
>
> Input PDB file: step5_assembly.pdb
> Output PDB file: amber.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.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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Received on Tue May 08 2012 - 12:00:06 PDT
