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<br>Dear Users ! <br><br>Thanks for the mail , now i fixed it <br><br>i have a general doubt,<br><br>i saw the path of gromacs <br> /usr/local/gromacs-4.5.3/share/top<br><br>there for the three point water model only spc216.gro is there is this common for <br>all , ie ., spc , spc/e and tip3p.<br><br><br><div>> Date: Mon, 10 Oct 2011 07:02:04 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] error_in topology<br>> <br>> <br>> <br>> balaji nagarajan wrote:<br>> > Dear Users !<br>> > <br>> > I have a problem in generating the topology of the attached molecule as pdb.<br>> > <br>> > earlier i have done using the same pdb for solvating the structure using <br>> > spc and spce water box ,<br>> > <br>> > there was no such error when i do for TIP4P and oplsaa force field i got <br>> > the error<br>> > <br>> > as follows<br>> > <br>> > -------------------------------------------------------<br>> > Program grompp, VERSION 4.5.3<br>> > Source code file: grompp.c, line: 523<br>> > <br>> > Fatal error:<br>> > number of coordinates in coordinate file (1AKI_solv.gro, 4164)<br>> > does not match topology (topol.top, 5527)<br>> > --------------------------------------------------------------------<br>> > <br>> > I used the following lines to do that<br>> > <br>> > pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water tip4p<br>> > editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic<br>> > genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top<br>> <br>> You told pdb2gmx to write the TIP4P topology into your .top, but then you used a <br>> 3-point water model. You need to solvate with tip4p.gro.<br>> <br>> -Justin<br>> <br>> > grompp -f sub.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr<br>> > mdrun -v -deffnm em<br>> > <br>> > in the grompp it says the error , how to solve this , and it comes only <br>> > for tip4p not for other water models.<br>> > <br>> > thanks in advance<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>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div> </div></body>
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