[gmx-users] Capping residues
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 8 02:48:09 CEST 2010
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>> 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>> 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>>> 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>>>> 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>>>> 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>>
> <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>>>>> 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>>
> <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>>>>>
> 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>>
> <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>>>>,
> Discussion list for
> GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
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> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>>>>
>
> > 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
> 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> <http://vt.edu> |
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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> |
> (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
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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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