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gmx-users,</SPAN><SPAN lang=EN-US
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pdb2gmx seems to be strange that</SPAN><SPAN lang=EN-US
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<P class=MsoNormal
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net charge of the first group (N terminal) is not decimal number.</SPAN><SPAN
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style="FONT-FAMILY: 'MS UI Gothic'; mso-bidi-font-family: 'ＭＳ Ｐゴシック'; mso-font-kerning: 0pt; mso-bidi-font-size: 10.5pt">I
put </SPAN><SPAN lang=EN-US
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(attached file) into pdb2gmx<o:p></o:p></SPAN></P>
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style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'; mso-bidi-font-size: 10.5pt">and
chose ffG53a6 for the force field.</SPAN><SPAN lang=EN-US
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style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'; mso-bidi-font-size: 10.5pt">In
the topol.top (attached file) obtained,</SPAN><SPAN lang=EN-US
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style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'; mso-bidi-font-size: 10.5pt">the
first and second charge groups are as follows:</SPAN><SPAN lang=EN-US
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<P class=MsoNormal
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align=left><SPAN lang=EN-US
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style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'; mso-bidi-font-size: 10.5pt">[
atoms ]<BR>; nr type resnr residue
atom cgnr charge mass typeB chargeB massB<BR>;
residue 33 LEU rtp LEU q +1.0<BR>
1 NL 33 LEU
N 1 0.129 14.0067 ; qtot
0.129<BR> 2 H
33 LEU H1 1 0.248
1.008 ; qtot 0.377<BR>
3 H
33 LEU H2 1 0.248 1.008
; qtot 0.625<BR> 4 H
33 LEU H3 1 0.248 1.008
; qtot 0.873<BR>
5 CH1 33 LEU CA 2 0.127 13.019
; qtot 1<BR>
6 CH2 33 LEU CB 2
0 14.027 ; qtot 1<o:p></o:p></SPAN></P>
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<P class=MsoNormal
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am sorry if I misunderstand it.<o:p></o:p></SPAN></P>
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align=left><SPAN lang=EN-US><FONT face=Century>Best regards,</FONT></SPAN></P>
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align=left><SPAN lang=EN-US><FONT
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