[gmx-users] Capping residues
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 8 04:14:17 CEST 2010
Sai Pooja wrote:
> Hi Justin,
>
> I do not have the problem of extra hydrogens or a net charge on the NAC
> group.
>
The net charge is not on NAC, it's on the entire peptide. If you're not seeing
it, that makes the bug even more troubling, since it's sporadic. Are you using
the latest git version, or an older one? If it's older, that may help track
down the code change that is causing problems.
> In relation to the other bugs you have mentioned, would it be a good
> idea to start a project with this git version of gromacs? The topology
> file I have now looks fine but I may be missing certain irregularities.
> Is there a good way to check?
>
I would never recommend using a git version for production work. It is under
continual development (thanks to the hard work of the developers!) and as such,
small (or large) bugs may get occasionally introduced, or new features added or
modified. I would only suggest using a git version for actual data collection
if it fixes a specific bug that was a problem for you and the git version fixes
it and is stable.
As far as checking, I have no idea. The test suite needs to be developed
further before there is a useful set of tools for validating a GROMACS installation.
> Is there another safe way to use the charmm forcefield with
> gromacs(without gromacs)?
>
Supposedly the CHARMM implementation in GROMACS is stable, but maybe changes in
the code have given rise to the bugs I'm suspecting. I can't even get a
topology for lysozyme; there are a host of errors which are concerning to me.
Otherwise use the CHARMM program, or even NAMD.
-Justin
> Pooja
>
>
> On Wed, Jul 7, 2010 at 8:48 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Sai Pooja wrote:
>
> This probably is my ignorance but the error and the "bug" goes
> when I replaced CBX with NAC everywhere.
>
>
>
> I would suggest filing a bugzilla. I was able to reproduce your
> problem. If nothing else, pdb2gmx should not be name-specific.
> Something very weird is going on. More troubling, the topology
> that pdb2gmx generated for me with NAC as the C-terminal cap had a
> broken net charge of +0.960 - it appears that pdb2gmx is adding
> double hydrogens to the backbone amides - both H and HN.
>
> With the impending release of Gromacs 4.5, this could be a very
> problematic bug.
>
> -Justin
>
>
> On Wed, Jul 7, 2010 at 6:09 PM, Sai Pooja <saipooja at gmail.com
> <mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
> <mailto:saipooja at gmail.com>>> wrote:
>
> 1. I have only added entries in the .rtp files. Do I need to add
> them in .hdb and .tdb files too? Could I simply define a new
> terminal in the aminoacids.c.tdb file?
>
> For your reference:
>
> *Initial PDB file*
> ATOM 1 C ACE 1 12.532 -0.094 26.546 1.00
> 2.10 FR1 C
> ATOM 2 O ACE 1 13.443 -0.213 25.696 1.00
> 1.60 FR1 O
> ATOM 3 CH3 ACE 1 12.782 -0.027 28.022 1.00
> 2.17 FR1 C
> ATOM 4 HH31 ACE 1 13.138 -0.995 28.375 1.00
> 2.17 FR1 H
> ATOM 5 HH32 ACE 1 11.856 0.230 28.537 1.00
> 2.17 FR1 H
> ATOM 6 HH33 ACE 1 13.535 0.733 28.228 1.00
> 2.17 FR1 H
> ATOM 7 N VAL 2 11.255 -0.021 26.193 1.00
> 1.60 FR1 N
> ATOM 8 CA VAL 2 10.854 -0.210 24.846 1.00
> 2.37 FR1 C
> ATOM 9 C VAL 2 11.022 1.197 24.222 1.00
> 2.10 FR1 C
> ATOM 10 O VAL 2 10.340 2.192 24.528 1.00
> 1.60 FR1 O
> ATOM 11 CB VAL 2 9.401 -0.679 24.711 1.00
> 2.37 FR1 C
> ATOM 12 CG1 VAL 2 9.113 -0.953 23.274 1.00
> 2.17 FR1 C
> ATOM 13 CG2 VAL 2 9.141 -1.946 25.547 1.00
> 2.17 FR1 C
> ATOM 14 H VAL 2 10.636 0.148 26.935 1.00
> 0.80 FR1 H
> ATOM 15 N GLN 3 12.113 1.241 23.470 1.00
> 1.60 FR1 ATOM 16 H GLN 3 12.656
> 0.425 23.466 1.00 0.80 FR1 ATOM 17 CA GLN
> 3 12.533 2.509 22.812 1.00 2.37 FR1 ATOM
> 18 CB GLN 3 13.982 2.287 22.560 1.00 2.23
> FR1 ATOM 19 CG GLN 3 14.807 3.474
> 22.166 1.00 2.23 FR1 ATOM 20 CD GLN 3
> 16.219 3.156 22.441 1.00 2.10 FR1 ATOM
> 21 OE1 GLN 3 16.635 2.341 23.295 1.00 1.60
> FR1 ATOM 22 NE2 GLN 3 17.095 3.710 21.642
> 1.00 1.60 FR1 ATOM 23 HE21 GLN 3
> 18.031 3.421 21.665 1.00 0.80 FR1 ATOM 24
> HE22 GLN 3 16.790 4.446 21.071 1.00 0.80
> FR1 ATOM 25 C GLN 3 11.689 2.846 21.556
> 1.00 2.10 FR1 ATOM 26 O GLN 3
> 11.395 3.988 21.389 1.00 1.60 FR1 ATOM 27
> N LEU 4 11.403 1.872 20.676 1.00 1.60
> FR1 ATOM 28 H LEU 4 11.747 0.959 20.767
> 1.00 0.80 FR1 ATOM 29 CA LEU 4
> 10.606 2.121 19.473 1.00 2.37 FR1 ATOM 30
> CB LEU 4 11.011 1.111 18.398 1.00 2.23
> FR1 ATOM 31 CG LEU 4 12.501 1.073 18.020
> 1.00 2.37 FR1 ATOM 32 CD1 LEU 4
> 12.869 -0.185 17.207 1.00 2.17 FR1 ATOM 33
> CD2 LEU 4 12.893 2.344 17.332 1.00 2.17
> FR1 ATOM 34 C LEU 4 9.082 2.102 19.484
> 1.00 2.10 FR1 ATOM 35 O LEU 4
> 8.400 1.579 20.374 1.00 1.60 FR1 ATOM 36 N
> CBX 5 8.609 2.722 18.430 1.00 1.60 FR1
> ATOM 37 H CBX 5 9.198 3.338 17.946 1.00
> 0.80 FR1
> ATOM 38 CH3 CBX 5 7.176 2.594 17.895 1.00
> 2.17 FR1
> ATOM 39 HH31 CBX 5 6.785 1.605 18.135 1.00
> 2.17 FR1 H
> ATOM 40 HH32 CBX 5 7.178 2.732 16.814 1.00
> 2.17 FR1 H
> ATOM 41 HH33 CBX 5 6.547 3.355 18.357 1.00
> 2.17 FR1
>
>
> *Changes in .rtp file*
> [ ACE ] [ atoms ]
> CH3 CT3 -0.270 0
> HH31 HA 0.090 0
> HH32 HA 0.090 0
> HH33 HA 0.090 0
> C C 0.510 1
> O O -0.510 1
> [ bonds ]
> C CH3
> C +N
> CH3 HH31
> CH3 HH32
> CH3 HH33
> O C
> [ impropers ]
> C CH3 +N O
> [ CBX ]
> [ atoms ]
> N NH1 -0.470 1 HN H
> 0.310 1 CH3 CT3 -0.110 1 HH31
> HA 0.090 1 HH32 HA 0.090 1
> HH33 HA 0.090 1 [ bonds ]
> -C N
> N HN
> N CH3
> CH3 HH31
> CH3 HH32
> CH3 HH33
> [ impropers ]
> N -C CH3 HN
> -C CH3 N -O
>
> *command:*
> pdb2gmx -f F1.pdb -q F1clean.pdb -nocmap -v -ss -ter -o
> work.gro -p
> work.top
>
> *.gro file from pdb2gmx*
> 1ACE CH3 1 1.278 -0.003 2.802
> 1ACE HH31 2 1.314 -0.100 2.838
> 1ACE HH32 3 1.186 0.023 2.854
> 1ACE HH33 4 1.354 0.073 2.823
> 1ACE C 5 1.253 -0.009 2.655
> 1ACE O 6 1.344 -0.021 2.570
> 2VAL N 7 1.125 -0.002 2.619
> 2VAL HN 8 1.064 0.015 2.694
> 2VAL CA 9 1.085 -0.021 2.485
> 2VAL HA 10 1.142 -0.094 2.447
> 2VAL CB 11 0.940 -0.068 2.471
> 2VAL HB 12 0.879 0.005 2.503
> 2VAL CG1 13 0.911 -0.095 2.327
> 2VAL HG11 14 0.817 -0.126 2.318
> 2VAL HG12 15 0.925 -0.012 2.274
> 2VAL HG13 16 0.973 -0.167 2.294
> 2VAL CG2 17 0.914 -0.195 2.555
> 2VAL HG21 18 0.819 -0.223 2.544
> 2VAL HG22 19 0.974 -0.268 2.523
> 2VAL HG23 20 0.932 -0.175 2.651
> 2VAL C 21 1.102 0.120 2.422
> 2VAL O 22 1.034 0.219 2.453
> 3GLN N 23 1.211 0.124 2.347
> 3GLN HN 24 1.266 0.043 2.347
> 3GLN CA 25 1.253 0.251 2.281
> 3GLN HA 26 1.240 0.331 2.340
> 3GLN CB 27 1.398 0.229 2.256
> 3GLN HB1 28 1.437 0.191 2.340
> 3GLN HB2 29 1.406 0.161 2.183
> 3GLN CG 30 1.481 0.347 2.217
> 3GLN HG1 31 1.469 0.367 2.119
> 3GLN HG2 32 1.453 0.428 2.270
> 3GLN CD 33 1.622 0.316 2.244
> 3GLN OE1 34 1.663 0.234 2.329
> 3GLN NE2 35 1.709 0.371 2.164
> 3GLN HE21 36 1.803 0.342 2.167
> 3GLN HE22 37 1.679 0.445 2.107
> 3GLN C 38 1.169 0.285 2.156
> 3GLN O 39 1.140 0.399 2.139
> 4LEU N 40 1.140 0.187 2.068
> 4LEU HN 41 1.175 0.096 2.077
> 4LEU CA 42 1.061 0.212 1.947
> 4LEU HA 43 1.085 0.309 1.937
> 4LEU CB 44 1.101 0.111 1.840
> 4LEU HB1 45 1.076 0.020 1.873
> 4LEU HB2 46 1.049 0.133 1.757
> 4LEU CG 47 1.250 0.107 1.802
> 4LEU HG 48 1.305 0.103 1.886
> 4LEU CD1 49 1.287 -0.019 1.721
> 4LEU HD11 50 1.384 -0.017 1.699
> 4LEU HD12 51 1.267 -0.100 1.775
> 4LEU HD13 52 1.234 -0.020 1.636
> 4LEU CD2 53 1.289 0.234 1.733
> 4LEU HD21 54 1.386 0.231 1.709
> 4LEU HD22 55 1.235 0.246 1.650
> 4LEU HD23 56 1.273 0.312 1.794
> 4LEU C 57 0.908 0.210 1.948
> 4LEU OT1 58 0.840 0.158 2.037
> 4LEU OT2 59 0.845 0.235 1.830
> 4LEU HT2 60 0.746 0.231 1.844
> 5CBX N 61 0.861 0.272 1.843
> 5CBX HN 62 0.920 0.334 1.795
> 5CBX CH3 63 0.718 0.259 1.789
> 5CBX HH31 64 0.678 0.161 1.814
> 5CBX HH32 65 0.718 0.273 1.681
> 5CBX HH33 66 0.655 0.336 1.836
> 1.14840 0.71270 1.21755
>
>
>
>
>
>
> *PDB file from pdb2gmx using -q option*
>
> TITLE Gromacs Runs On Most of All Computer Systems
> MODEL 1
> ATOM 1 C ACE 1 12.532 -0.094 26.546 1.00
> 2.10 C
> ATOM 2 O ACE 1 13.443 -0.213 25.696 1.00
> 1.60 O
> ATOM 3 CH3 ACE 1 12.782 -0.027 28.022 1.00
> 2.17 C
> ATOM 4 1HH3 ACE 1 13.138 -0.995 28.375 1.00
> 2.17 H
> ATOM 5 2HH3 ACE 1 11.856 0.230 28.537 1.00
> 2.17 H
> ATOM 6 3HH3 ACE 1 13.535 0.733 28.228 1.00
> 2.17 H
> ATOM 7 N VAL 2 11.255 -0.021 26.193 1.00
> 1.60 N
> ATOM 8 CA VAL 2 10.854 -0.210 24.846 1.00
> 2.37 C
> ATOM 9 C VAL 2 11.022 1.197 24.222 1.00
> 2.10 C
> ATOM 10 O VAL 2 10.340 2.192 24.528 1.00
> 1.60 O
> ATOM 11 CB VAL 2 9.401 -0.679 24.711 1.00
> 2.37 C
> ATOM 12 CG1 VAL 2 9.113 -0.953 23.274 1.00
> 2.17 C
> ATOM 13 CG2 VAL 2 9.141 -1.946 25.547 1.00
> 2.17 C
> ATOM 14 H VAL 2 10.636 0.148 26.935 1.00
> 0.80 H
> ATOM 15 N GLN 3 12.113 1.241 23.470 1.00
> 1.60 N
> ATOM 16 H GLN 3 12.656 0.425 23.466 1.00
> 0.80 H
> ATOM 17 CA GLN 3 12.533 2.509 22.812 1.00
> 2.37 C
> ATOM 18 CB GLN 3 13.982 2.287 22.560 1.00
> 2.23 C
> ATOM 19 CG GLN 3 14.807 3.474 22.166 1.00
> 2.23 C
> ATOM 20 CD GLN 3 16.219 3.156 22.441 1.00
> 2.10 C
> ATOM 21 OE1 GLN 3 16.635 2.341 23.295 1.00
> 1.60 O
> ATOM 22 NE2 GLN 3 17.095 3.710 21.642 1.00
> 1.60 N
> ATOM 23 1HE2 GLN 3 18.031 3.421 21.665 1.00
> 0.80 HE
> ATOM 24 2HE2 GLN 3 16.790 4.446 21.071 1.00
> 0.80 HE
> ATOM 25 C GLN 3 11.689 2.846 21.556 1.00
> 2.10 C
> ATOM 26 O GLN 3 11.395 3.988 21.389 1.00
> 1.60 O
> ATOM 27 N LEU 4 11.403 1.872 20.676 1.00
> 1.60 N
> ATOM 28 H LEU 4 11.747 0.959 20.767 1.00
> 0.80 H
> ATOM 29 CA LEU 4 10.606 2.121 19.473 1.00
> 2.37 C
> ATOM 30 CB LEU 4 11.011 1.111 18.398 1.00
> 2.23 C
> ATOM 31 CG LEU 4 12.501 1.073 18.020 1.00
> 2.37 C
> ATOM 32 CD1 LEU 4 12.869 -0.185 17.207 1.00
> 2.17 C
> ATOM 33 CD2 LEU 4 12.893 2.344 17.332 1.00
> 2.17 C
> ATOM 34 C LEU 4 9.082 2.102 19.484 1.00
> 2.10 C
> ATOM 35 O LEU 4 8.400 1.579 20.374 1.00
> 1.60 O
> ATOM 36 N CBX 5 8.609 2.722 18.430 1.00
> 1.60 N
> ATOM 37 H CBX 5 9.198 3.338 17.946 1.00
> 0.80 H
> ATOM 38 CH3 CBX 5 7.176 2.594 17.895 1.00
> 2.17 C
> ATOM 39 1HH3 CBX 5 6.785 1.605 18.135 1.00
> 2.17 H
> ATOM 40 2HH3 CBX 5 7.178 2.732 16.814 1.00
> 2.17 H
> ATOM 41 3HH3 CBX 5 6.547 3.355 18.357 1.00
> 2.17 H
> TER
> ENDMDL
>
>
> These files were generated using the option -COOH for C terminal.
> *However, if "none" is chosen, I get the error:*
>
> Fatal error:
> There is a dangling bond at at least one of the terminal ends.
> Select a proper terminal entry.
> For more information and tips for troubleshooting, please
> check the
> GROMACS
> I have used Mark's definitions for capping residues in the
> rtp file.
>
>
> Pooja
>
>
> On Wed, Jul 7, 2010 at 4:47 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Sai Pooja wrote:
>
> I checked again and the error does not go. Please
> read the
> steps below.
>
> The pdb file I started off with did not have any
> hydrogens.
> However, the way I had specified the capping residues
> in the
> .rtp file (SEE MARK'S MAIL), I had to specify
> hydrogens in
> the pdb file for the capping residues. So I used pymol to
> add hydrogens to my pdb file. I then used this file with
> charmm force field. However, pymol had added hydrogens
> everywhere and this was different from the definition
> of the
> standard residues defined in the .rtp file. I could not
> directly use -ignh because I needed the hydrogens for the
> capping residues. So I created a file that contained the
> hydrogens on the capping residues only. This resolved the
> error related to hydrogens.
>
>
> Probably an easier and more reliable approach would
> simply be to
> create an .hdb entry for your capping groups.
>
>
>
> Error-from previous mail-NOT RESOLVED
> (Fatal error:
> There is a dangling bond at at least one of the
> terminal ends.
> Select a proper terminal entry.
> For more information and tips for troubleshooting,
> please
> check the
> GROMACS
> I have used Mark's definitions for capping residues in
> the rtp file.
>
> In the pdb file, this is what the capping residues
> look like:
>
> ATOM 33 N CBX 5 8.609 2.722 18.430
> 1.00 1.60 FR1
> ATOM 34 H CBX 5 9.198 3.338 17.946
> 1.00 0.80 FR1
> ATOM 35 CH3 CBX 5 7.176 2.594 17.895
> 1.00 2.17 FR1
>
>
> Maybe this is just showing up incorrectly in my mail
> client, but
> I wonder if that CH3 is somehow misaligned and therefore not
> correctly identified. I presume that you changed the residue
> name in the .rtp file accordingly? I suppose the error
> message
> would be different (something like "residue not found") but I
> just want to make sure. Mark's entry used NAC.
>
>
> ATOM 1 CH3 ACE 1 12.782 -0.027 28.022
> 1.00 2.17 FR1
> ATOM 2 C ACE 1 12.532 -0.094 26.546
> 1.00 2.10 FR1
> ATOM 3 O ACE 1 13.443 -0.213 25.696
> 1.00 1.60 FR1 )
>
> The error stated in the previous mail(quoted above)
> occurred
> when I chose "none" for the both terminals or the
> carboxylic
> terminal option (using -ter). It worked fine if I chose
> "none" at the N terminal and any other option except
> "none"
> at the carboxylic acid terminal. So I chose "none" at N
> terminal and some option randomly at the carboxylic acid
> terminal. As expected, it adds a terminal at that end
> of the
> residue before my capping residue which is something
> I DONT
> want. I
>
>
> So does pdb2gmx somehow add the C-terminal cap after the
> carboxylate terminus?
>
>
> havent been able to find a way around it. Interestingly,
> when I generate a pdb file using -q, and open that
> pdb file
> in pymol, I dont get the terminal carboxylic acid that
> pdb2gmx gives in the .gro file.
>
>
> So the cap is applied properly in that structure?
>
>
> I am not sure how to correct this. One way would be to
> remove those entries from the final .gro and .top
> file but
> not sure if that would be right.
>
>
> This all sounds very fishy. This may be worth a bugzilla
> entry,
> but only if you can build the structure in a very sound way,
> probably using .hdb entries (or an appropriate all-atom
> structure, which you've yet to demonstrate).
>
> -Justin
>
> Pooja
>
>
>
>
>
>
>
> On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
>
>
>
> Sai Pooja wrote:
>
> Follow-up. It is easy to make it work. Just
> needed to
> be more
> rigorous. Thank you.
>
>
> It would be helpful if you describe what you mean.
> This
> error
> message is new to me, and appears to reflect new
> mechanics in the
> upcoming Gromacs release. If you describe what the
> problem was, how
> you resolved it, what your pdb2gmx command line
> was, and
> anything
> else that might be useful, that would likely help
> others
> solve this
> issue in the future.
>
> -Justin
>
> On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja
> <saipooja at gmail.com <mailto:saipooja at gmail.com>
> <mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
> <mailto:saipooja at gmail.com
> <mailto:saipooja at gmail.com>
> <mailto:saipooja at gmail.com
> <mailto:saipooja at gmail.com>>> <mailto:saipooja at gmail.com
> <mailto:saipooja at gmail.com>
>
> <mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
>
> <mailto:saipooja at gmail.com
> <mailto:saipooja at gmail.com>
> <mailto:saipooja at gmail.com
> <mailto:saipooja at gmail.com>>>>> wrote:
>
> I used -ter option and selected "none" for both
> terminal ends
> but I
> still get this error:
>
> Fatal error:
> There is a dangling bond at at least one of the
> terminal ends.
> Select a proper terminal entry.
> For more information and tips for
> troubleshooting,
> please
> check the
> GROMACS
> I have used Mark's definitions for capping
> residues in the
> rtp file.
>
> In the pdb file, this is what the capping
> residues
> look like:
>
> ATOM 33 N CBX 5 8.609 2.722
> 18.430 1.00
> 1.60 FR1
> ATOM 34 H CBX 5 9.198 3.338
> 17.946 1.00
> 0.80 FR1
> ATOM 35 CH3 CBX 5 7.176 2.594
> 17.895 1.00
> 2.17 FR1
>
> ATOM 1 CH3 ACE 1 12.782 -0.027
> 28.022 1.00
> 2.17 FR1
> ATOM 2 C ACE 1 12.532 -0.094
> 26.546 1.00
> 2.10 FR1
> ATOM 3 O ACE 1 13.443 -0.213
> 25.696 1.00
> 1.60 FR1
>
>
>
>
>
>
> On Fri, Jul 2, 2010 at 10:50 AM, Justin A.
> Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>> wrote:
>
>
>
> Sai Pooja wrote:
>
> Thanks Marks. I tried it but this
> is what
> I get:
>
> Fatal error:
> atom N not found in buiding block
> 1ACE while
> combining tdb
> and rtp
> For more information and tips for
> troubleshooting, please
> check the GROMACS
> website at
> http://www.gromacs.org/Documentation/Errors
>
> Do I need to edit the aminoacids.n.tdb
> file as well?
>
>
> What are you choosing as your termini
> when running
> pdb2gmx? It
> should be "none," since by capping, you are
> not choosing a
> protonation state for the N- and C-termini.
>
> -Justin
>
>
> Pooja
>
>
>
> On Thu, Jul 1, 2010 at 11:39 PM,
> Mark Abraham
> <mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>
> <mailto:mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>>
> <mailto:mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>
> <mailto:mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>>>
> <mailto:mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au> <mailto:mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>>
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> <mailto:mark.abraham at anu.edu.au>>>>>> wrote:
>
>
>
> ----- Original Message -----
> From: Sai Pooja
> <saipooja at gmail.com <mailto:saipooja at gmail.com>
> <mailto:saipooja at gmail.com <mailto:saipooja at gmail.com>>
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> Date: Friday, July 2, 2010 7:28
> Subject: Re: [gmx-users] Capping
> residues
> To: jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
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> Discussion list for
> GROMACS users
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>
> > I am sorry if I did not frame the
> question
> correctly,
> but putting
> it very simply, is there a way
> to use
> capping residues
> with the
> charmm forcefield if the
> residues are
> --COCH3 and
> NHCH3?
>
> Yes - you edit a copy of the
> .rtp file
> in your working
> directory and
> add whatever you want. Here's what I
> use in CHARMM
>
> [ ACE ]
> [ atoms ]
> CH3 CT3 -0.270 0
> HH31 HA 0.090 0
> HH32 HA 0.090 0
> HH33 HA 0.090 0
> C C 0.510 1
> O O -0.510 1
> [ bonds ]
> C CH3
> C +N
> CH3 HH31
> CH3 HH32
> CH3 HH33
> O C
> [ impropers ]
> C CH3 +N O
>
> [ NAC ]
> [ atoms ]
> N NH1 -0.470 1
> HN H 0.310 1
> CH3 CT3 -0.110 1
> HH31 HA 0.090 1
> HH32 HA 0.090 1
> HH33 HA 0.090 1
> [ bonds ]
> -C N
> N HN
> N CH3
> CH3 HH31
> CH3 HH32
> CH3 HH33
>
> [ impropers ]
> N -C CH3 HN
> -C CH3 N -O
>
> Mark
> --
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> --
> ========================================
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> Justin A. Lemkul
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> ICTAS Doctoral Scholar
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> Department of Biochemistry
> Virginia Tech
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>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
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> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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