On Tue, 2015-03-03 at 11:43 +0530, Harshala Haldankar wrote:
> hi,
>
> I am new to Amber software and want to simulate a* helical peptide *in
> water using ff12Sb force field. I need to cap this peptide with ACE and NME
> groups.
> I have generated the helical peptide using Chimera and capped it using DS
> visualizer. However, the parameter and topology files are not generated and
> am I get the following error:
>
> FATAL: Atom.R<NME 19>.A<C 7> does not have a type
> Failed to generate parameter.
>
> Can someone suggest how to get rid of this error.
You need to make sure that the atom names in NME match the atom names in
the Amber residue libraries. In particular, NME is defined in
$AMBERHOME/dat/leap/lib/aminont12.lib. The entry looks like this (to
start):
!entry.NME.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"N" "N" 0 1 131072 1 7 -0.415700
"H" "H" 0 1 131072 2 1 0.271900
"CH3" "CT" 0 1 131072 3 6 -0.149000
"HH31" "H1" 0 1 131072 4 1 0.097600
"HH32" "H1" 0 1 131072 5 1 0.097600
"HH33" "H1" 0 1 131072 6 1 0.097600
!entry.NME.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"N" "N" 0 -1 0.0
"H" "H" 0 -1 0.0
"CH3" "CT" 0 -1 0.0
"HH31" "H1" 0 -1 0.0
"HH32" "H1" 0 -1 0.0
"HH33" "H1" 0 -1 0.0
So you can see that there is no atom named "C" in that template. If
that's the methyl carbon, you need to rename it "CH3" in the PDB file
(but be sure that the columns remain correct, since the PDB is strict
column-based format).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 03 2015 - 05:30:02 PST
