<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Nope, theoretically impossible.<DIV><BR class="khtml-block-placeholder"></DIV><DIV>You'll have to start by getting get rid of the inifinite force. Move the atoms manually, or use soft-core interactions.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV><BR class="khtml-block-placeholder"><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On Sep 7, 2005, at 1:02 PM, Naser, Md Abu wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><P><FONT size="2">Hi All,<BR> <BR> <BR> <BR> I have an atom with infinite maximum force in a protein. Is any protocol of energy minimization that can handle this situation?<BR> <BR> With regards,<BR> abu<BR> <BR> <BR> <BR> <BR> <BR> -----Original Message-----<BR> From: <A href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</A> on behalf of Naser, Md Abu<BR> Sent: Tue 9/6/2005 11:13 AM<BR> To: <A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR> Subject: [gmx-users] Segmentation fault<BR> <BR> Hi All,<BR> <BR> I have included a new amino acid- phosphoserine(PSE) in rtp file. Although,I included the amino acid in ffG43a1.hdb and<BR> <BR> pdb2gmx -f xxx.pdb -o xxx.gro -ignh -missing -p xxx.top, gives<BR> <BR> WARNING: atom H is missing in residue PSE 67 in the pdb file<BR> You might need to add atom H to the hydrogen database of residue PSE<BR> in the file ff???.hdb<BR> <BR> When I run mdrun, i am getting segmentation fault.<BR> <BR> <BR> Can anyone advise me where might be problem?<BR> <BR> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR> in ffG43a1.rtp<BR> [ PSE ]<BR> <BR> [ atoms ]<BR> N N -0.28000 0<BR> H H 0.28000 0<BR> CA CH1 0.00000 1<BR> CB CH2 0.15000 2<BR> OG OA -0.54800 2<BR> P P 0.79800 2<BR> O1P OM -0.80000 2<BR> O2P OM -0.80000 2<BR> O3P OM -0.80000 2<BR> C C 0.380 3<BR> O O -0.380 3<BR> [ bonds ]<BR> N H gb_2 <BR> N CA gb_20 <BR> CA C gb_26 <BR> C O gb_4 <BR> C +N gb_9 <BR> CA CB gb_26 <BR> CB OG gb_17 <BR> P O1P ga_23<BR> P O2P ga_23<BR> P O3P ga_23<BR> P OG ga_27 <BR> [ angles ]<BR> ; ai aj ak gromos type<BR> -C N H ga_31 <BR> H N CA ga_17 <BR> -C N CA ga_30 <BR> N CA C ga_12 <BR> CA C +N ga_18 <BR> CA C O ga_29 <BR> O C +N ga_32 <BR> N CA CB ga_12 <BR> C CA CB ga_12 <BR> CA CB OG ga_12 <BR> OG P O1P ga_23<BR> OG P O2P ga_23<BR> OG P O3P ga_23<BR> CB OG P ga_27<BR> O1P P O2P ga_28<BR> O1P P O3P ga_28<BR> O2P P O3P ga_28<BR> [ impropers ]<BR> ; ai aj ak al gromos type<BR> N -C CA H gi_1 <BR> C CA +N O gi_1 <BR> CA N C CB gi_2 <BR> [ dihedrals ]<BR> ; ai aj ak al gromos type<BR> -CA -C N CA gd_4 <BR> -C N CA C gd_19 <BR> N CA C +N gd_20 <BR> N CA CB OG gd_17 <BR> CA CB OG P gd_12<BR> CB OG P O1P gd_11<BR> CB OG P O2P gd_11<BR> CB OG P O3P gd_11<BR> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR> in ffG43a1.hdb<BR> PSE 2<BR> 1 1 N -C CA <BR> 1 2 OG CB CA<BR> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR> <BR> <BR> <BR> </FONT> </P><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV> </BLOCKQUOTE></DIV><BR></DIV></DIV></BODY></HTML>