Re: [gmx-users] Dummy Problem.
Anthony Cruz wrote: Hi Mark: Thank you for your interest. No, it does not work without the constraint. the dummy atom still collapsing with the ND atom. Also I try: [ constraint ] ; ai aj funct b0 ND CON 2 0.064381 But grompp give me the following error: Cleaning up constraints and constant bonded interactions with dummy particles ERROR: Cannot have constraint (86-87) with dummy atom (87) Fatal error: There were 1 dummy atoms involved in constraints OK, that's expected behaviour if you read the relevant manual section. Also I try to put all the [ dummies2 ] and [ constraints ] after the bonding information with the same result, the collapsing of the dummy atom. What could be the problem??? I'm guessing wildly here, but maybe EM doesn't work with dummy atoms. Try an EM without the dummy atom and then do position restrained MD with the dummy atom and see how you go. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dummy Problem.
Hi Mark: Thank you for your interest. No, it does not work without the constraint. the dummy atom still collapsing with the ND atom. Also I try: [ constraint ] ; ai aj funct b0 ND CON 20.064381 But grompp give me the following error: Cleaning up constraints and constant bonded interactions with dummy particles ERROR: Cannot have constraint (86-87) with dummy atom (87) Fatal error: There were 1 dummy atoms involved in constraints Also I try to put all the [ dummies2 ] and [ constraints ] after the bonding information with the same result, the collapsing of the dummy atom. What could be the problem??? Anthony On Tuesday 06 February 2007 8:08 pm, Mark Abraham wrote: > Anthony Cruz wrote: > > Hi Users: > > > > > > In my topology before all the bonded information I add the following > > lines with the appropiate numbers: > > > > [ dummies2 ] > > ;Dummy from functa > > CONNDOE 1 0.064381 > > > > [ constraint ] > > ; ai aj funct b0 > > ND OE 2 0.12032 > > > > The problem is that the dummy colapse with the ND atom during the EM. > > What could be the problem? I need to add the dummies2 section in my > > topology if it is present in the residue topology and it is present in my > > pdb??? > > Does it work without the constraint? > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dummy Problem.
Anthony Cruz wrote: Hi Users: In my topology before all the bonded information I add the following lines with the appropiate numbers: [ dummies2 ] ;Dummy from functa CONNDOE 1 0.064381 [ constraint ] ; ai aj funct b0 ND OE 2 0.12032 The problem is that the dummy colapse with the ND atom during the EM. What could be the problem? I need to add the dummies2 section in my topology if it is present in the residue topology and it is present in my pdb??? Does it work without the constraint? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dummy Problem.
Hi Users: I have a question about dummy atoms. I try to simulate a protein that have a cysteine modified with a NO group. I found a NO model that have 3 sites, one at each atom and other in the center of mass (Biophys. Chem. 98 (2002) 183). [ SNC ] [ atoms ] N N-0.28000 0 H H 0.28000 0 CA CH1 0.0 1 CB CH2 0.0 1 SG S 0.0 1 ND NON-0.25000 2 CON COM 0.59500 2 OE NOO-0.34500 2 C C 0.380 3 O O -0.380 3 [ bonds ] N Hgb_2 NCAgb_20 CA Cgb_26 C Ogb_4 C+Ngb_9 CACBgb_26 CBSGgb_30 SGNDgb_49 [ angles ] ; aiajak gromos type -C N H ga_31 H NCA ga_17 -C NCA ga_30 NCA C ga_12 CA C+N ga_18 CA C O ga_29 O C+N ga_32 NCACB ga_12 CCACB ga_12 CACBSG ga_15 CBSGND ga_47 SGNDOE ga_48 [ impropers ] ; aiajakal gromos type N-CCA H gi_1 CCA+N O gi_1 CA N CCB gi_2 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_4 -C NCA C gd_19 NCA C+N gd_20 NCACBSG gd_17 CACBSGND gd_13 CBSGNDOE gd_22 In my topology before all the bonded information I add the following lines with the appropiate numbers: [ dummies2 ] ;Dummy from functa CONNDOE 1 0.064381 [ constraint ] ; ai aj funct b0 ND OE 2 0.12032 The problem is that the dummy colapse with the ND atom during the EM. What could be the problem? I need to add the dummies2 section in my topology if it is present in the residue topology and it is present in my pdb??? Thanks Anthony ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
