<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span><br></span></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;"> <div dir="ltr"> <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> Wednesday, June 6, 2012 4:08 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Atomtype OW_tip4p not found<br> </font> </div> <br>
<br><br>On 6/6/12 7:36 AM, Amir Abbasi wrote:<br>><br>><br>> --------------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Amir Abbasi <<a ymailto="mailto:amir.abbasi69@yahoo.com" href="mailto:amir.abbasi69@yahoo.com">amir.abbasi69@yahoo.com</a>>; Discussion list for GROMACS users<br>> <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Wednesday, June 6, 2012 3:58 PM<br>> *Subject:* Re: [gmx-users] Atomtype OW_tip4p not found<br>><br>><br>><br>> On 6/6/12 7:19 AM, Amir Abbasi wrote:<br>> > Hi!<br>> > I use tleap to generate topology file of a RNA molecule with parmbsc0 ff. Then I<br>> > generate .gro and .top files of that with <a target="_blank"
href="http://amb2gmx.pl">amb2gmx.pl</a> <<a href="http://amb2gmx.pl" target="_blank">http://amb2gmx.pl</a>>.<br>> > I'm manually add this lines to .top file<br>> > ; Include water topology<br>> > #include "amber99sb.ff/tip4p.itp"<br>> ><br>> > ; Include topology for ions<br>> > #include "amber99sb.ff/ions.itp"<br>> > but after running this code:<br>> ><br>> > grompp -f ions.mdp -c ribozyme_solv.gro -p ribozyme.top -o ions.tpr<br>> > I've got this error message:<br>> ><br>> > Program grompp, VERSION 4.5.5<br>> > Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1166<br>> ><br>> > Fatal error:<br>> > Atomtype OW_tip4p not found<br>> ><br>> > what should I do?<br>> ><br>><br>> If I recall my Amber
evolution correctly, parmbsc0 and Amber99SB are different<br>> entities, so you may have some inconsistencies in your force field calls. Which<br>> of the Amber force fields in Gromacs have you called (earlier in the topology)?<br>> The OW_tip4p atom type exists in Amber99SB, so I don't know the origin of the<br>> error.<br>><br>> -Justin<br>><br>> I've Removed these lines from .top file<br>><br>> ; Include water topology<br>> #include "amber99sb.ff/tip4p.itp"<br>><br>> ; Include topology for ions<br>> #include "amber99sb.ff/ions.itp"<br>> But this error occured:<br>><br>> Program grompp, VERSION 4.5.5<br>> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1987<br>><br>> Fatal error:<br>> No such moleculetype SOL<br>><br>> what's the true way to add solvent molecules to my system?<br>> I want to use parmbsc0 ff that's not included in gromacs and I use it with
amb2gmx<br>><br><br>Please answer the question posted above by posting a relevant topology snippet. <br> It's hard (impossible) to help you while working in the dark. Presumably you <br>have some force field you are calling - what is it?<br><br>Removal of these lines will not solve the problem, as you can see. You need to <br>#include a water model of some sort to define what parameters water will have, <br>but it needs to be consistent with whatever force field you are using or have <br>otherwise constructed.<br><br>-Justin<br>this is my topology file (generated by amb2gmx_dihed_old.pl):<br><br>; rna.top created by rdparm2gmx.pl Thu May 24 19:07:56 IRDT 2012<br><br>[ defaults ]<br>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>1
2 yes 0.5 0.8333<br><br>[ atomtypes ]<br>;name bond_type mass charge ptype sigma epsilon<br>HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00<br>NC NC 0.0000 0.0000 A 3.25000e-01 7.11280e-01<br>H5 H5 0.0000 0.0000 A 2.42146e-01
6.27600e-02<br>N2 N2 0.0000 0.0000 A 3.25000e-01 7.11280e-01<br>CB CB 0.0000 0.0000 A 3.39967e-01 3.59824e-01<br>CK CK 0.0000 0.0000 A 3.39967e-01 3.59824e-01<br>N* N* 0.0000 0.0000 A 3.25000e-01 7.11280e-01<br>OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01<br>CT
CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01<br>C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01<br>NB NB 0.0000 0.0000 A 3.25000e-01 7.11280e-01<br>CA CA 0.0000 0.0000 A 3.39967e-01 3.59824e-01<br>OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01<br>NA NA 0.0000 0.0000 A
3.25000e-01 7.11280e-01<br>O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01<br>CM CM 0.0000 0.0000 A 3.39967e-01 3.59824e-01<br>H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02<br>O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01<br>P P 0.0000 0.0000 A 3.74177e-01
8.36800e-01<br>H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02<br>HA HA 0.0000 0.0000 A 2.59964e-01 6.27600e-02<br>H4 H4 0.0000 0.0000 A 2.51055e-01 6.27600e-02<br>H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02<br><br>[ moleculetype ]<br>; Name nrexcl<br>solute 3<br>there is not any force field included. I want to
use parmbsc0 ff thats not included in gromacs. I build topology file in tleap (part of ambertools) then convert it to gromacs topology file.<br><br><br> </div> </div> </div></body></html>