<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>HI Justin,</span></div><div><br><span></span></div><div><span>I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions.</span></div><div>So I do not think ions addition will help. And I double-checked the angles, bonds, .... mentioned in the ffoplsaabon.itp, they are there.</div><div>So I do not know any other files I may need to modify.</div><div><br></div><div>Thanks,</div><div><br></div><div>yao<br></div><div><br></div><div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight:
bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Monday, August 29, 2011 3:41 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] OPLS-AA Unknown Atomtype<br></font><br><br><br>Yao Yao wrote:<br>> Hi Justin,<br>> <br>> Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp,<br>> but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like,<br>> <br>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#<br>> checking input for internal consistency...<br>> processing topology...<br>> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp<br>> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp<br>> Opening library file
/share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp<br>> Generated 338253 of the 338253 non-bonded parameter combinations<br>> Generating 1-4 interactions: fudge = 0.5<br>> Generated 338253 of the 338253 1-4 parameter combinations<br>> <br>> ERROR 1 [file cro.top, line 37]:<br>> No default Bond types<br>> <br>> <br>> ERROR 2 [file cro.top, line 71]:<br>> No default Angle types<br>> <br>> <br>> ERROR 3 [file cro.top, line 72]:<br>> No default Angle types<br>> <br>> <br>> ERROR 4 [file cro.top, line 85]:<br>> No default Angle types<br>> <br>> <br>> ERROR 5 [file cro.top, line 91]:<br>> No default Ryckaert-Bell. types<br>> <br>> <br>> ERROR 6 [file cro.top, line 92]:<br>> No default Ryckaert-Bell. types<br>> <br>> <br>> ERROR 7 [file cro.top, line 93]:<br>> No default Ryckaert-Bell. types<br>> <br>> <br>>
ERROR 8 [file cro.top, line 108]:<br>> No default Ryckaert-Bell. types<br>> <br>> <br>> ERROR 9 [file cro.top, line 112]:<br>> No default Proper Dih. types<br>> <br>> <br>> ERROR 10 [file cro.top, line 113]:<br>> No default Proper Dih. types<br>> <br>> <br>> ERROR 11 [file cro.top, line 114]:<br>> No default Proper Dih. types<br>> <br>> Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp<br>> Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp<br>> Excluding 3 bonded neighbours molecule type 'Protein'<br>> Excluding 2 bonded neighbours molecule type 'SOL'<br>> Excluding 2 bonded neighbours molecule type 'SOL'<br>> <br>> NOTE 1 [file cro.top, line 142]:<br>> System has non-zero total charge: -1.022478e+00<br>> <br><br>This total charge suggests that your topology is badly broken.<br><br>> <br>>
processing coordinates...<br>> double-checking input for internal consistency...<br>> renumbering atomtypes...<br>> converting bonded parameters...<br>> <br>> There was 1 note<br>> <br>> -------------------------------------------------------<br>> Program grompp, VERSION 4.0.7<br>> Source code file: grompp.c, line: 986<br>> <br>> Fatal error:<br>> There were 11 errors in input file(s)<br>> -----------------------------------------------<br>> <br>> I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values?<br>> <br><br>If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again.<br><br>-Justin<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 ymailto="mailto:gmx-users@gromacs.org" href="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 ymailto="mailto:gmx-users-request@gromacs.org"
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