<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>I mean if I still want to use the introduced amber03 ff, when I solvate it as normal, it asks for gbsa.itp,</span></div><div><br><span></span></div><div><span>----------</span></div><div>Fatal error:<br>Library file gbsa.itp not found in current dir nor in default directories.<br>(You can set the directories to search with the GMXLIB path variable)<br><br><span></span></div><div><span>----------<br></span></div><div><br></div><div>So is there any other file I need to change?</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> Tuesday, September 6, 2011 3:21 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] gbsa.itp problem<br></font><br><br><br>Yao Yao wrote:<br>> Hi Justin,<br>> <br>> Thanks for your reply. Is there a way I can use explicit water to get rid of the error?<br>> <br><br>Solvate as you would any normal system and don't try to use force field files from newer versions.<br><br>-Justin<br><br>> Thanks,<br>> <br>> Yao<br>> <br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Yao Yao <<a
ymailto="mailto:yao0o@ymail.com" href="mailto:yao0o@ymail.com">yao0o@ymail.com</a>>; Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Tuesday, September 6, 2011 2:42 PM<br>> *Subject:* Re: [gmx-users] gbsa.itp problem<br>> <br>> <br>> <br>> Yao Yao wrote:<br>> > Hi All,<br>> ><br>> > when I grompp for energy minimization, I met the error like,<br>> ><br>> > --------------------------------------------------------------<br>> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#<br>> > checking input for internal consistency...<br>> > processing topology...<br>> > Opening library file /share/apps/gromacs407/share/gromacs/top/ffamber03.itp<br>> > Opening library file
/share/apps/gromacs407/share/gromacs/top/ffnonbonded.itp<br>> ><br>> > WARNING 1 [file ffnonbonded.itp, line 38]:<br>> > Overriding atomtype NA<br>> ><br>> > Opening library file /share/apps/gromacs407/share/gromacs/top/ffbonded.itp<br>> > Opening library file /share/apps/gromacs407/share/gromacs/top/gbsa.itp<br>> ><br>> > ERROR 1 [file gbsa.itp, line 1]:<br>> > Invalid directive implicit_genborn_params<br>> ><br>> ><br>> > -------------------------------------------------------<br>> > Program grompp, VERSION 4.0.7<br>> > Source code file: toppush.c, line: 756<br>> ><br>> > Fatal error:<br>> > Unknown bond_atomtype 0.172<br>> > -------------------------------------------------------<br>> ><br>> > Since in
the version 4.0.7 there is no gbsa.itp, I simply copied the file with the same name from gmx 4.5-4 and introduced ffamber03 force field into 4.0.7.<br>> > I understand updating to 4.5.X will solve this problem, but for testing my QMMM semi-empirical implementation, I have to use gmx version 4.0.7, at least for now.<br>> > So I am wondering if there is any way I can solve it in 4.0.7.<br>> ><br>> <br>> You can't do implicit solvent simulations with a version < 4.5.<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>> <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 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
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