<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><BR>in windows , I use ultraedit, in linux ,use vi <BR><BR><A class=plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A><BR><BR>--- <B>12年6月3日，周日, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> 写道：<BR>
<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9:19<BR><BR>
<DIV class=plainMail><BR><BR>On 6/3/12 9:16 AM, xi zhao wrote:<BR>><BR>> I use Ultraedit to produce new part and paste the files; we add a residue name<BR>> and corresponding atom type and interaction parameters<BR>><BR><BR>Having never used a commercial text editor, I don't know if its integrity. What <BR>happens if you use a different editor, like vi/emacs (Linux/Mac) or Notepad <BR>(Windows)? What operating system are you using?<BR><BR>The only times I've had pdb2gmx die when reading atom types are when the line <BR>endings are bad, so I would strongly suspect this is your issue.<BR><BR>-Justin<BR><BR>> 4<BR>> <<A href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" target=_blank>http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844</A>><BR>><BR>> ---
*12年6月3日，周日, Justin A. Lemkul /<<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>>/* 写道：<BR>><BR>><BR>> 发件人: Justin A. Lemkul <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu" ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>><BR>> 主题: Re: [gmx-users] Atomtype 1<BR>> 收件人: "Discussion list for GROMACS users" <<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>> 日期: 2012年6月3日,周日,下午8:46<BR>><BR>><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>> ><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<BR>> 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,<BR>>
and to what files? Are you using a plain text editor that properly treats<BR>> 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
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href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A><BR>> <<A href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" target=_blank>http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org</A>>.<BR>> Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank>http://www.gromacs.org/Support/Mailing_Lists</A><BR>><BR><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>--
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