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!
<
http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
Virus-free.
www.avg.com
<
http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 17 2019 - 08:30:02 PDT
