Thanks Yun,<div><br></div><div>Have a look at <a href="http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx">http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx</a> so you may have tips of how to improve you check. One thing I recorded that makes diff is that amber input files have 6 decimals of precision and PDB/GRO only 3.</div>
<div><br></div><div>Not knowing exactly what you did, but it sounds that 0.05% (for total pot energy?) is OK.</div><div><br></div><div>Alan</div><div><br></div><div><br><br><div class="gmail_quote">On 15 September 2011 06:18, 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 Alan,<br><br>For example, in the Glycam_06g.dat file, you can find:<br>........<br>OH-CG-CG-OS 1 -1.10 0.0 -1<br>
........<br><br>So this dihedral parameter has a force constant of -1.10, and this is what I mean by "GLYCAM force field assigns negative force constants to some dihedrals".<br>
<br>I did try the GMX45 approach, and using the conversion factor 4.184, I got a difference of about 0.05%. I am not sure if this is caused not setting step size in the sander minimization.<br><br>Regards,<br>Yun<br><br>
<br><br><br><br><br><br>Date: Tue, 13 Sep 2011 12:03:10 +0100<br>
From: Alan <<a href="mailto:alanwilter@gmail.com" target="_blank">alanwilter@gmail.com</a>><br>
Subject: Re: [gmx-users] Re: <a href="http://amb2gmx.pl/" target="_blank">amb2gmx.pl</a> to convert GLYCAM topology<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAEznbznq98PbHjdR1SMPOgdTz_pGFqsk40iZLfPQ7-NiZywJ4A@mail.gmail.com" target="_blank">CAEznbznq98PbHjdR1SMPOgdTz_pGFqsk40iZLfPQ7-NiZywJ4A@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<div><div></div><div class="h5"><br>
<br>
Hi Yun,<br>
<br>
Have you read <a href="http://ambermd.org/formats.html" target="_blank">http://ambermd.org/formats.html</a>?<br>
<br>
In particular, this note:<br>
<br>
"""<br>
NOTE: *the atom numbers in the following arrays that describe bonds, angles,<br>
and dihedrals are coordinate array indexes for runtime speed. The true atom<br>
number equals the absolute value of the number divided by three, plus one.<br>
In the case of the dihedrals, if the fourth atom is negative, this implies<br>
that the dihedral is an improper. If the third atom is negative, this<br>
implies that the end group interations are to be ignored. End group<br>
interactions are ignored, for example, in dihedrals of various ring systems<br>
(to prevent double counting of 1-4 interactions) and in multiterm dihedrals.<br>
*<br>
"""<br>
<br>
I may be failing to understand what you mean by "GLYCAM force field assigns<br>
negative force constants to some dihedrals".<br>
<br>
Anyway, since GMX 4.5 can go without RB convertions, you can do this:<br>
<br>
acpype -x disac.inpcrd -p disac.prmtop --gmx45<br>
<br>
If you have sander, you can do just one step of EM and compare against one<br>
step EM with GMX. Do the proper conversions and Energies diff should be <<br>
0.001%.<br>
<br>
Cheers,<br>
<br>
Alan<br>
<br>
On 12 September 2011 21:21, Yun Shi <<a href="mailto:yunshi09@gmail.com" target="_blank">yunshi09@gmail.com</a>> wrote:<br>
<br>
> Hi all,<br>
><br>
> I am not a CS person, but I did find something in acpype.py as<br>
><br>
> .............<br>
> if phase in [0, 180]:<br>
> properDihedralsGmx45.append([</div></div><blockquote class="gmail_quote"><div><div></div><div class="h5">item[0].atoms, phaseRaw,<br>
> kPhi, period])<br>
> if not self.gmx45:<br>
> if kPhi > 0: V[period] = 2 * kPhi * cal<br>
> if period == 1:<br>
> C[0] += 0.5 * V[period]<br>
> if phase == 0:<br>
> C[1] -= 0.5 * V[period]<br>
> else:<br>
> C[1] += 0.5 * V[period]<br>
> elif period == 2:<br>
> ......................<br>
><br>
> kPhi here seems to be the dihedral force constant, and it seems if kPhi <<br>
> 0, no value will be assigned to C[0], C[1], C[2] ...<br>
><br>
> I wonder if the negative dihedral force constants problem could be solved<br>
> by changing 'kPhi > 0' to 'kPhi != 0' for acpype?<br>
><br>
> Thanks,<br>
><br>
> Yun<br>
><br>
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Date: Tue, 13 Sep 2011 16:46:44 +0530<br>
From: om prakash <<a href="mailto:ombioinfo@gmail.com" target="_blank">ombioinfo@gmail.com</a>><br>
Subject: [gmx-users] Unsubscribe me Please<div class="im"><br>
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