[AMBER] Mg2+_preparation_general_rule

From: Antonio Amber Carlesso <antonio.amber.carlesso.gmail.com>
Date: Wed, 17 Apr 2019 17:27:11 +0200

Hi all,

We are interested in performing a MD simulations of a protein where on its
kinase active is co-crystallized ADP and Mg2+



At the final stage, when we were thinking everything proceed smoothly, we
receive this message..

> saveamberparm complex complex.prmtop complex.inpcrd

Checking Unit.

Building topology.

Building atom parameters.



*Error: For atom (.R<MG 1368>.A<MG 1>) could not find vdW (or other)
parameters for type (Mg2+)*



*Error: For atom (.R<MG 1370>.A<MG 1>) could not find vdW (or other)
parameters for type (Mg2+)*



Warning: Parameter file was not saved.



Any idea how to successfully finished the first stage of this MD
investigation?

 [ I suppose the parameters for Mg2+ were present by looking here:

> list

A A3 A5 ACE ADA ADB AG
AL

ALA AN ARG ASH ASN ASP Ag
BA

BR Be C C3 C5 CA CALA
CARG

CASN CASP CCYS CCYX CD CE CGLN
CGLU

CGLY CHCL3BOX CHID CHIE CHIP CHIS CHYP
CILE

CL CLEU CLYS CMET CN CO CPHE
CPRO

CR CS CSER CTHR CTRP CTYR CU
CU1

CVAL CYM CYS CYX Ce Cl- Cr
DA

DA3 DA5 DAN DC DC3 DC4 DC5
DCN

DG DG3 DG5 DGN DT DT3 DT5
DTN

Dy EU EU3 Er F FB3 FB3BOX
FB4

FB4BOX FE FE2 G G3 G5 GD3
GLH

GLN GLU GLY GN H3O+ HE+ HG
HID

HIE HIP HIS HOH HYP HZ+ Hf
ILE

IN IOD K K+ LA LEU LI
LU

LYN LYS MEOHBOX MET *MG* MN NA
     NALA

NARG NASN NASP NCYS NCYX NGLN NGLU
NGLY

NH4 NHE NHID NHIE NHIP NHIS NI
NILE

NLEU NLYS NMABOX NME NMET NPHE NPRO
NSER

NTHR NTRP NTYR NVAL Na+ Nd OHE
OP3

OPC OPC3BOX OPCBOX PB PD PHE PL3
POL3BOX

PR PRO PT Pu QSPCFWBOX RB Ra
S2P

SER SM SPC SPCBOX SPCFWBOX SPF SPG
SR

Sm Sn T2P T4E TB THR TIP3PBOX
TIP3PFBOX

TIP4PBOX TIP4PEWBOXTIP5PBOX TL TP3 TP4 TP5
TPF

TRP TYR Th Tl Tm U U3
U4+

U5 UN V2+ VAL WAT Y YB2
ZN

Zr complex frcmod14SBgaff parm10

]





Thank you all!

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Received on Wed Apr 17 2019 - 08:30:02 PDT
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