<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>in fact, the pdb2gmx still hang. I modified the atomtypes.atp , <BR>aminoacids.rtp , ffbonded.itp, ffnonbonded.itp , <BR>aminoacids.hdb, residuetypes.dat<IMG class=pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"><BR>,morever, now the pdb2gmx_d even does not the standard protein structure. </DIV>
<DIV><BR>--- <B>12年6月3日，周日, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> 写道：<BR></DIV>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>发件人: Justin A. Lemkul <jalemkul@vt.edu><BR>主题: Re: [gmx-users] Atomtype 1<BR>收件人: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>日期: 2012年6月3日,周日,下午8:46<BR><BR>
<DIV class=plainMail><BR><BR>On 6/3/12 8:24 AM, xi zhao wrote:<BR>> Dear gmx-users:<BR>> I add a new residue in *rtp ,according to<BR>> <A href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" target=_blank>http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</A>,<BR>> and modified corresponding files :such as atp, hdb , after making a full copy of<BR>> the installed forcefield in woring diectory.<BR>> When pdb2gmx_d<BR>> appeared "<BR>> All occupancies are one<BR>> Opening force field file ./amber99sbr.ff/atomtypes.atp<BR>> Atomtype 1"<BR>> Please give me suggestions<BR><BR>Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines?<BR><BR>-Justin<BR><BR>-- ========================================<BR><BR>Justin A. Lemkul, Ph.D.<BR>Research
Scientist<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>-- gmx-users mailing list <A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <A
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