Date: Wed, 17 Apr 2019 18:53:47 +0200
Hi all,
I fixed by load the appropriate frcmod files for divalent ions by checking
this table!
[image: ions.PNG]
thank you anyway!
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On Wed, Apr 17, 2019 at 5:27 PM Antonio Amber Carlesso <
antonio.amber.carlesso.gmail.com> wrote:
> 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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(image/png attachment: ions.PNG)
