[AMBER] SCEE and SCNB GLYCAM_06 values with amber11 top crd files

From: Kepa K. Burusco <kekoburgo.yahoo.es>
Date: Wed, 18 Apr 2012 18:55:09 +0100 (BST)



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


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.


Kepa K. Burusco

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Received on Wed Apr 18 2012 - 11:00:03 PDT
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