Hi,
Not sure, in your message I see that the fields for the water oxygen O are not well aligned.
HTH
--------------------------------------------------------------------
Stéphane Abel, Ph.D.
CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : 石坪江梨花 [13lb010p.rikkyo.ac.jp]
Envoyé : samedi 19 avril 2014 12:22
À : amber.ambermd.org
Objet : [AMBER] 【AMBER12】Including water when using General Amber Force Field leaprc.gaff
Dear all,
I have tried HOH for the residue name for water,
HETATM1 O HOH 1 -5.382 16.838 -57.659 1.00 0.00 O
HETATM2 H1 HOH 1 -4.602 17.179 -58.121 1.00 0.00 H
HETATM3 H2 HOH 1 -5.047 16.021 -57.260 1.00 0.00 H
END
but there was the following error .
-- residue 1: duplicate [ HO] atoms (total 3)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Unknown residue: number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: sequence: 1
Created a new atom named: HO within residue: .R< 1>
total atoms in file: 3
The file contained 1 atoms not in residue templates
I'm really not sure what the problem is.
Please tell me how to modify it.
*Regards,*
Erika
--
*―――――――――――――――――――――*
石坪 江梨花
立教大学 理学研究科化学専攻
博士課程前期課程 1年
理論創薬・分子設計 常盤研究室
〒171-8501 東京都豊島区西池袋3-34-1
4号館4230教室
Email: 13lb010p.rikkyo.ac.jp
erika.i.rikkyo.ac.jp
*―――――――――――――――――――――*
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Received on Sat Apr 19 2014 - 04:00:03 PDT
