[gmx-users] Capping residues
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 8 03:11:59 CEST 2010
As a follow-up, it appears that there are several problems with the CHARMM
implementation. I will file a bugzilla with a few other things I found. There
are a number of errors in the aminoacids.rtp file that cause problems. Most of
all, I can't even get pdb2gmx to generate a CHARMM topology for lysozyme. If
that fails, then we're in trouble :)
-Justin
Justin A. Lemkul 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>> 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
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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>>>>>
>>
>> > 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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>>
>> -- Quaerendo Invenietis-Seek
>> and you
>> shall discover.
>>
>>
>> --
>> ========================================
>>
>> 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> |
>>
>> (540) 231-9080
>>
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>> -- Quaerendo Invenietis-Seek and you shall
>> discover.
>>
>>
>>
>>
>> -- Quaerendo Invenietis-Seek and you shall
>> discover.
>>
>>
>> -- ========================================
>>
>> 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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>>
>>
>> -- Quaerendo Invenietis-Seek and you shall
>> discover.
>>
>>
>> -- ========================================
>>
>> 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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>>
>>
>>
>> -- Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>
--
========================================
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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