<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thank you, sir. That's nice of Gromacs to automatically assign new atom types from an input pdb file. I check out the link as well. <BR><BR>--- On <B>Mon, 2/21/11, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> wrote:<BR>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Justin A. Lemkul <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] on force fields<BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Monday, February 21, 2011, 10:41 AM<BR><BR>
<DIV class=plainMail><BR><BR>Mr Bernard Ramos wrote:<BR>> Thanks for the reply on my first querry. I have another one. If I add a NEW atom type in *.atp file, will Gromacs automatically recognize this atom type? <BR><BR>Theoretically, yes, provided that you supply any corresponding parameters in, e.g., ffnonbonded.itp and ffbonded.itp. However, there is an unresolved bug related to atomtype assignment that may be relevant:<BR><BR><A href="http://redmine.gromacs.org/issues/618" target=_blank>http://redmine.gromacs.org/issues/618</A><BR><BR>It seems to me that any alterations to the .atp file cause things to break down, so do not be surprised if there are problems.<BR><BR>-Justin<BR><BR>> Thanks.<BR>> <BR>> <BR>> --- On *Wed, 2/16/11, Mark Abraham /<<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=Mark.Abraham@anu.edu.au" ymailto="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</A>>/* wrote:<BR>>
<BR>> <BR>> From: Mark Abraham <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=Mark.Abraham@anu.edu.au" ymailto="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</A>><BR>> Subject: Re: [gmx-users] on force fields<BR>> To: "Discussion list for GROMACS users" <<A href="http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>> Date: Wednesday, February 16, 2011, 1:53 PM<BR>> <BR>> On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote:<BR>>> Hi everyone!<BR>>> I need to update the gromos force field 53A6 with the new force<BR>>> field 53ACARBO (JCC 10 NOV 2010).<BR>>> 1. I will have
to change the parameter values in the file<BR>>> ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these<BR>>> the only files that I need to update if I need to switch to a new<BR>>> force field?<BR>>> <BR>> <BR>> You should make a copy of the whole force field directory into your<BR>> working directory, rename the new directory suitably, make a<BR>> suitable change to forcefield.doc, and then edit .itp files<BR>> suitably. This means you're leaving your reference version untouched<BR>> and can edit locally to your heart's content, and can be sure you're<BR>> selecting the right force field with pdb2gmx and/or in your .top file.<BR>> <BR>>> 2.
The new force field 53ACARBO has a new gromos functional form<BR>>> for select torsional potentials. How to I go over implementing<BR>>> this in gromos?<BR>>> <BR>> <BR>> Preferably as a sum of existing functional forms. Or use tabulated<BR>> bonded interactions (see manual and wiki).<BR>> <BR>> Mark<BR>> <BR>> -----Inline Attachment Follows-----<BR>> <BR>> -- gmx-users mailing list <A href="http://us.mc527.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://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org"
target=_blank>http://us.mc527.mail.yahoo.com/mc/compose?to=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<BR>> <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<BR>> www interface or send it to <A href="http://us.mc527.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://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org"
target=_blank>http://us.mc527.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<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<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://us.mc527.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 href="http://us.mc527.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>Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank>http://www.gromacs.org/Support/Mailing_Lists</A><BR></DIV></BLOCKQUOTE></td></tr></table><br>