I am using Amber 16 on Ubuntu 16.04, I followed your suggestions but got
something (Could not see the N). I tried something new instead of using my
PDB files, in xleap, I started from Thr residue, means
>edit THR
and then added the CU atoms to the structure and then
>saveoff THR TCU.lib
after that manually I changed all THR inside of this lib file to TCU. by
this trick problem with the lib file solved (I do not get atom type error
anymore).
for TCU.frcmod (for CU ions) I used the file in the tutorial (
http://ambermd.org/tutorials/advanced/tutorial1_adv/index.htm):
# modifications to force field for poplar plastocyanin
MASS
SM 32.06
CU 65.36
BOND
NB-CU 70.000 2.05000 #kludge by JRS
CU-S 70.000 2.10000 #kludge by JRS
CU-SM 70.000 2.90000 #for pcy
CT-SM 222.000 1.81000 #met(aa)
ANGLE
CU-NB-CV 50.000 126.700 #JRS estimate
CU-NB-CR 50.000 126.700 #JRS estimate
CU-NB-CP 50.000 126.700 #JRS estimate
CU-NB-CC 50.000 126.700 #JRS estimate
CU-SM-CT 50.000 120.000 #JRS estimate
CU-S -CT 50.000 120.000 #JRS estimate
CU-S -C2 50.000 120.000 #JRS estimate
CU-S -C3 50.000 120.000 #JRS estimate
NB-CU-NB 10.000 110.000 #dac estimate
NB-CU-SM 10.000 110.000 #dac estimate
NB-CU-S 10.000 110.000 #dac estimate
SM-CU-S 10.000 110.000 #dac estimate
CU-SM-CT 50.000 120.000 #JRS estimate
CT-CT-SM 50.000 114.700 #met(aa)
HC-CT-SM 35.000 109.500
H1-CT-SM 35.000 109.500
CT-SM-CT 62.000 98.900 #MET(OL)
DIHE
X -NB-CU-X 1 0.000 180.000 3.000
X -CU-SM-X 1 0.000 180.000 3.000
X -CU-S -X 1 0.000 180.000 3.000
X -CT-SM-X 3 1.000 0.000 3.000
NONBON
CU 2.20 0.200
SM 2.00 0.200
The new error that I am getting is
For atom: .R<YCU 138>.A<Cu22 22> Could not find vdW (or other)
parameters for type: Cu
and this my leap script:
source $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff10
loadoff YCU1.lib
loadamberparams YCU.frcmod
loadAmberParams frcmod
set default PBradii bondi
mods = loadAmberParams frcmod.ionsjc_tip3p
mol = loadpdb H4-DNA-Mutated-clean-YAG-test.pdb
#addions mol Na+ 0
#addions mol Cl- 0
#addions2 mol Na+ 34
#addions2 mol Cl- 34
solvateBox mol OPCBOX 4.22 iso
saveamberparm mol H4-DNA-OPC-FF10.top H4-DNA-OPC-FF10.crd
quit
What should I do now?
Thank you for you help.
On Thu, Aug 31, 2017 at 3:50 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> You should be able to click the draw box top right, then click on one
> atom and draw to the next before releasing.
>
> If that doesn't work, what kind of hardware/OS are you running on?
>
> It would be faster to
>
> > x = loadpdb the.pdb
>
> > bondbydistance x
>
> > edit x
>
> Then delete the extra bonds, and draw the missing ones.
>
> Bill
>
>
> On 8/31/17 10:11 AM, Parviz Seifpanahi Shabane wrote:
> > Yes, I did, this what I am getting (attached image) after loading TMN.pdb
> > to xleap.
> >
> > On Thu, Aug 31, 2017 at 1:02 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> I only see 1 N atom in the pdb below, and it appears in xleap.
> >>
> >> I was able to draw bonds between MN and O, N.
> >>
> >> Did you click on 'Draw' on the top of the xleap editor?
> >>
> >> Bill
> >>
> >> On 8/31/17 8:11 AM, Parviz Seifpanahi Shabane wrote:
> >>> Dear AMBER users,
> >>> I need to add the highly charged ion (-120 e) to my system in certain
> >> place
> >>> in my PDB file before running simulation, I am following this tutorial:
> >>> http://ambermd.org/tutorials/advanced/tutorial1_adv/index.htm
> >>> I picked the residue which has the best position (Threonine (Thr)) for
> my
> >>> purpose and created the new residue named TMN by adding the Mn ion to
> it.
> >>> this my TMN.pdb file:
> >>>
> >>> ATOM 525 N TMN B 96 55.589 87.183 6.224 0.00 0.00
> >> N
> >>> ATOM 526 CA TMN B 96 56.332 86.013 5.728 0.00 0.00
> >> C
> >>> ATOM 527 C TMN B 96 57.725 86.436 5.230 0.00 0.00
> >> C
> >>> ATOM 528 O TMN B 96 57.865 87.357 4.412 0.00 0.00
> >> O
> >>> ATOM 529 CB TMN B 96 55.580 85.363 4.578 0.00 0.00
> >> C
> >>> ATOM 530 CG2 TMN B 96 56.358 84.123 3.985 0.00 0.00
> >> C
> >>> ATOM 531 OG1 TMN B 96 54.305 84.932 5.050 0.00 0.00
> >> O
> >>> ATOM 908 H TMN B 96 54.624 87.243 5.931 0.00 0.00
> >> H
> >>> ATOM 909 HA TMN B 96 56.448 85.287 6.533 0.00 0.00
> >> H
> >>> ATOM 910 HB TMN B 96 55.451 86.086 3.773 0.00 0.00
> >> H
> >>> ATOM 911 HG21 TMN B 96 55.745 83.227 4.084 0.00 0.00
> >> H
> >>> ATOM 912 HG22 TMN B 96 56.575 84.299 2.931 0.00 0.00
> >> H
> >>> ATOM 913 HG23 TMN B 96 57.292 83.985 4.530 0.00 0.00
> >> H
> >>> ATOM 914 HG1 TMN B 96 54.425 84.288 5.752 0.00 0.00
> >> H
> >>> ATOM 13626 MN TMN B 96 55.100 90.254 3.700 0.97 51.89
> >> MN
> >>> problem is in editing step for creating TMN unit and library file I can
> >> not
> >>> see the Nitrogen (N) atoms (edit TMN.pdb) and I can not draw the bonds
> >>> correctly.
> >>> any idea?
> >>
> >> _______________________________________________
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> >>
> >
> >
> >
> >
> > _______________________________________________
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--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virgina Tech, Blacksburg, Va 24061
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Received on Fri Sep 01 2017 - 17:00:02 PDT
