1. You are correct that the behavior has changed over the last few
releases. Since the capability was new, things came up that were not
anticipated.
The best thing to do now is to use x/tleap in AmberTools12. A
well-patched AmberTools1.5 will also work. The "write14scale" keyword
only applies to sleap (not t or x leap), but use of sleap for this is
not recommended. If you use tleap and a recent AmberTools, you should
automatically get the entries as you need them.
2 & 3: If you use tleap from a recent AmberTools as described above,
the SCEE & SCNB entries present in the parameter file should be
automatically detected and written into the file. The correct values
for each interaction are automatically assigned.
On Wed, Apr 18, 2012 at 1:55 PM, Kepa K. Burusco <kekoburgo.yahoo.es> wrote:
> [18-IV-2012]
>
> Hi,
>
> I'm trying to run some MD calculations (in vacuo and in water) for glucose with amber11. Since I'm using GLYCAM_06 force field it is mandatory to use SCEE=1.0 and SCNB=1.0 values to override the by-default amber values.
>
> I have checked the amber reflector archives, amber tools manuals 11 and 12, and amber manuals 9, 10 and 11 and I have found different comments regarding SCEE and SCNB so I still have doubts.
>
> 1) AmberTools11 explains that "write14scale" option must be set to "on" to write SCEE and SCNB values to topology files. I have included this line in the leaprc file:
>
> ******************************************************
>
> source leaprc.GLYCAM_06
> source leaprc.ff99SB
> addatomtypes {
> { "D1" "O" "sp3" }
> { "D2" "H" "sp3" }
> { "D3" "O" "sp3" }
> { "D4" "H" "sp3" }
> }
> loadamberparams glucose_0.4.frcmod
> mol = loadMol2 glucose_0.4.mol2
> mol = sequence { mol }
> check mol
> solvatebox mol TIP3PBOX 10.0
> setbox mol vdw
> check mol
> set default PdbWriteCharges on
> savePDB mol glucose_WAT_0.4.pdb
> saveOff mol glucose_WAT_0.4.lib
> saveamberparm mol glucose_WAT_0.4.top glucose_WAT_0.4.crd
> quit
>
> *******************************************************
>
>
> But it is complaining for any for reason.
>
> Furthermore, when I created the top and crd files without setting write14scale to on, the topology file did not have the SCEE and SCNB values of 1.0 (head of sander minimization eergy file said that).
>
>
> *******************************************************************
>
> | Memory Use Allocated
> | Real 197258
> | Hollerith 6298
> | Integer 65216
> | Max Pairs 838973
> | nblistReal 22692
> | nblist Int 89522
> | Total 5624 kbytes
>
> | Note: 1-4 EEL scale factors were NOT found in the topology file.
> | Using default value of 1.2.
>
> | Note: 1-4 VDW scale factors were NOT found in the topology file.
> | Using default value of 2.0.
> | Duplicated 0 dihedrals
> | Duplicated 0 dihedrals
> *******************************************************************
>
>
> I have also a couple of questions:
>
> 2) For the "in vacuo" calculations ONLY glycam_06 forcefield is used so, is it correct to assume that when x/tleap reads the parameters file takes the SCEE and SCNB values and writes them into de top and crd files?
>
> 3) For the "in water" calculations, on the one hand "leaprc.GLYCAM_06" force field is needed for glucose and on the other hand "leaprc.ff99SB" is needed for TIP3P water unit. Mixing two force fields should not be a problem in amber11 (as I have read) because every system is treated with its own parameters. But should I include write14scale in the leaprc file or is it automatically detected?
>
> Any help will be welcome.
>
> Thanks!!
>
> Kepa K. Burusco
>
> *********************************************************************************************************
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Apr 18 2012 - 12:30:04 PDT
