On Wed, Jul 7, 2010 at 6:09 PM, Sai Pooja <saipo...@gmail.com
<mailto:saipo...@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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
<saipo...@gmail.com <mailto:saipo...@gmail.com>
<mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>> <mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>
<mailto:saipo...@gmail.com
<mailto:saipo...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>>> wrote:
----- Original Message -----
From: Sai Pooja <saipo...@gmail.com
<mailto:saipo...@gmail.com>
<mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>>
<mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>
<mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>>> <mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>
<mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>>
<mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com> <mailto:saipo...@gmail.com
<mailto:saipo...@gmail.com>>>>>
Date: Friday, July 2, 2010 7:28
Subject: Re: [gmx-users] Capping
residues
To: jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
<mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>,
Discussion list for
GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@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
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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.
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Quaerendo Invenietis-Seek and you shall discover.
