[gmx-users] Fatal error: Atomtype 'K' not found!

Erik Lindahl lindahl at sbc.su.se
Tue Oct 18 09:38:03 CEST 2005 

Hi,

Build one for opls - you simply shouldn't use ffgmx2 :-)

It's fairly trivial - I've attached a pentadecane (15 carbons) as an  
example.

Cheers,

Erik

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On Oct 18, 2005, at 4:14 AM, lmao wrote:

>
> Because I will include decane as solvent and I don't have topology  
> file for decane. Or I should build one. Thanks for your comment.
>
> mao
>
>>
>>
>> --===============0001768906==
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>>
>> Hi,
>>
>>
>>
>>> I was using Gromacs-3.2-1 for peptide simulations. I first used
>>> "pdb2gmx" to generate .gro file and I chose 5 from the following
>>> options to include H
>>> "Select the Force Field:
>>>  0: GROMOS96 43a1 Forcefield (official distribution)
>>>  1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
>>>  2: GROMOS96 43a2 Forcefield (development) (improved alkane  
>>> dihedrals)
>>>  3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>>>  4: Gromacs Forcefield (see manual)
>>>  5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new
>>> runs)"
>>>
>>
>> Question: I assume you read the entire last line here. Why do you
>> need to use ffgmx2 and not e.g. OPLS?
>>
>> Cheers,
>>
>> Erik
>>
>> -----------------------------------------------------------
>> Erik Lindahl  <lindahl at sbc.su.se>
>> Assistant Professor, Stockholm Bioinformatics Center
>> Stockholm University, SE 106 91 Stockholm
>> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
>>
>>
>>
>>
>>
>> --Apple-Mail-1-962561109
>> Content-Transfer-Encoding: quoted-printable
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>>     charset=ISO-8859-1
>>
>> <HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode:  
>> space; =
>> -khtml-line-break: after-white-space; "><DIV><BLOCKQUOTE =
>> type=3D"cite"></BLOCKQUOTE><DIV><FONT class=3D"Apple-style-span" =
>> color=3D"#0000DD">Hi,</FONT></DIV><BR><BR><BLOCKQUOTE  
>> type=3D"cite"><DIV =
>> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
>> margin-left: 0px; min-height: 14px; "></DIV><DIV style=3D"margin- 
>> top: =
>> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I  
>> was =
>> using Gromacs-3.2-1 for peptide simulations. I first used  
>> "pdb2gmx" to =
>> generate .gro file and I chose 5 from the following options to  
>> include =
>> H</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; margin- 
>> bottom: =
>> 0px; margin-left: 0px; ">"Select the Force Field:</DIV><DIV =
>> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
>> margin-left: 0px; "><SPAN class=3D"Apple-converted-space">=A0</ 
>> SPAN>0: =
>> GROMOS96 43a1 Forcefield (official distribution)</DIV><DIV =
>> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
>> margin-left: 0px; "><SPAN class=3D"Apple-converted-space">=A0</ 
>> SPAN>1: =
>> GROMOS96 43b1 Vacuum Forcefield (official distribution)</DIV><DIV =
>> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
>> margin-left: 0px; "><SPAN class=3D"Apple-converted-space">=A0</ 
>> SPAN>2: =
>> GROMOS96 43a2 Forcefield (development) (improved alkane =
>> dihedrals)</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
>> margin-bottom: 0px; margin-left: 0px; "><SPAN =
>> class=3D"Apple-converted-space">=A0</SPAN>3: OPLS-AA/L all-atom  
>> force =
>> field (2001 aminoacid dihedrals)</DIV><DIV style=3D"margin-top:  
>> 0px; =
>> margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN =
>> class=3D"Apple-converted-space">=A0</SPAN>4: Gromacs Forcefield  
>> (see =
>> manual)</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
>> margin-bottom: 0px; margin-left: 0px; "><SPAN =
>> class=3D"Apple-converted-space">=A0</SPAN>5: gmx Forcefield with =
>> hydrogens for NMR stuff (Do NOT use for new =
>> runs)"</DIV></BLOCKQUOTE></DIV><DIV><FONT class=3D"Apple-style- 
>> span" =
>> color=3D"#0000DD"><BR =
>> class=3D"khtml-block-placeholder"></FONT></DIV>Question: I assume  
>> you =
>> read the entire last line here. Why do you need to use ffgmx2 and  
>> not =
>> e.g. OPLS?<DIV><BR =
>> class=3D"khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR =
>> class=3D"khtml-block-placeholder"></ 
>> DIV><DIV>Erik<DIV><DIV><BR><DIV> =
>> <SPAN class=3D"Apple-style-span" style=3D"border-collapse:  
>> separate; =
>> border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family:  
>> Helvetica; =
>> font-size: 12px; font-style: normal; font-variant: normal; font- 
>> weight: =
>> normal; letter-spacing: normal; line-height: normal; text-align:  
>> auto; =
>> -khtml-text-decorations-in-effect: none; text-indent: 0px; =
>> -apple-text-size-adjust: auto; text-transform: none; orphans: 2; =
>> white-space: normal; widows: 2; word-spacing: 0px; =
>> "><DIV>----------------------------------------------------------- 
>> </DIV><D=
>> IV>Erik Lindahl=A0 &lt;<A =
>> href=3D"mailto:lindahl at sbc.su.se">lindahl at sbc.su.se</A>&gt;</ 
>> DIV><DIV>Assi=
>> stant Professor, Stockholm Bioinformatics Center</ 
>> DIV><DIV>Stockholm =
>> University, SE 106 91 Stockholm</DIV><DIV>Phone: +46 8 5537  
>> 8564=A0 =A0 =
>> =A0Fax: +46 8 5537 8214</DIV><DIV><BR =
>> class=3D"khtml-block-placeholder"></DIV><DIV><BR =
>> class=3D"khtml-block-placeholder"></DIV><BR =
>> class=3D"Apple-interchange-newline"></SPAN> =
>> </DIV><BR></DIV></DIV></DIV></BODY></HTML>=
>>
>> --Apple-Mail-1-962561109--
>>
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>>
>
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-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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