Hi Yun,<div><br></div><div>ACPYPE is working fine. What happens here is I choose the reproduce the exact values one sees in AMBER.</div><div><br></div><div>Now why GMX tip3p file choose a different value, I don't know.</div>
<div><br></div><div>Nevertheless, it's pretty simple to put whatever value you want there if you think you need.</div><div><br></div><div>Alan<br><br><div class="gmail_quote">On 26 September 2011 17:35, Yun Shi <span dir="ltr"><<a href="mailto:yunshi09@gmail.com">yunshi09@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi all,<br><br>I just noted that the tip3p water converted from amber format to gromacs format is<br><br>[ moleculetype ]<br>
; molname nrexcl ; TIP3P model<br> WAT 2<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass<br>
1 OW 1 WAT O 1 -0.834 16.00000<br> 2 HW 1 WAT H1 1 0.417 1.00800<br> 3 HW 1 WAT H2 1 0.417 1.00800<br><br>#ifdef FLEXIBLE<br>
[ bonds ]<br>; i j funct length force.c.<br>1 2 1 0.09572 462750.4 0.09572 462750.4<br>1 3 1 0.09572 462750.4 0.09572 462750.4<br><br>[ angles ]<br>; i j k funct angle force.c.<br>2 1 3 1 104.520 836.800 104.520 836.800<br>
#else<br>[ settles ]<br>; i j funct length<br>1 1 0.09572 0.15139<br><br>[ exclusions ]<br>1 2 3<br>2 1 3<br>3 1 2<br>#endif<br><br><br>while in amber99sb.ff/tip3p.itp. it is <br><br> moleculetype ]<br>
; molname nrexcl<br>SOL 2<br><br>[ atoms ]<br>; id at type res nr res name at name cg nr charge mass<br> 1 OW 1 SOL OW 1 -0.834 16.00000<br> 2 HW 1 SOL HW1 1 0.417 1.00800<br>
3 HW 1 SOL HW2 1 0.417 1.00800<br><br>#ifndef FLEXIBLE<br><br>[ settles ]<br>; OW funct doh dhh<br>1 1 0.09572 0.15139<br><br>[ exclusions ]<br>1 2 3<br>
2 1 3<br>3 1 2<br><br>#else<br><br>[ bonds ]<br>; i j funct length force_constant<br>1 2 1 0.09572 502416.0 0.09572 502416.0<br>1 3 1 0.09572 502416.0 0.09572 502416.0<br>
<br><br>[ angles ]<br>; i j k funct angle force_constant<br>2 1 3 1 104.52 628.02 104.52 628.02<br><br>#endif<br><br>So it seems that the force_constants for O-H bond and H-O-H angle are different? Does this mean amber and gromacs use different parameters for tip3p water? or it's just acpype is not working right?<br>
<br>Thanks,<br><font color="#888888">Yun<br>
</font><br>--<br>
gmx-users mailing list <a 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<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Alan Wilter SOUSA da SILVA, DSc<div>
Bioinformatician, UniProt - PANDA, EMBL-EBI<br>CB10 1SD, Hinxton, Cambridge, UK</div><div>+44 1223 49 4588</div><br>
</div>