[gmx-users] what is control atoms???
Mehreen Jan
mehreen_jan1990 at yahoo.com
Wed Feb 10 05:13:05 CET 2016
thank you sir!
what is control atoms in gromacs???how can we define control atoms???
reason of control atom????
--------------------------------------------
On Wed, 10/2/16, gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 48
To: gromacs.org_gmx-users at maillist.sys.kth.se
Received: Wednesday, 10 February, 2016, 7:27 AM
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Today's Topics:
1. difference between gmx energy and gmx
traj (Ray Chao)
2. Re: wrong number of control atoms (2
iso 3) on line: 2 3 N -C
-CA (Justin Lemkul)
3. Re: complex topology file (Justin
Lemkul)
4. Re: difference between gmx energy and
gmx traj (Justin Lemkul)
5. Re: add parameter (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Tue, 9 Feb 2016 17:24:42 -0500
From: Ray Chao <xiaoainisa at gmail.com>
To: gmx-users at gromacs.org
Subject: [gmx-users] difference between gmx energy and gmx
traj
Message-ID:
<CAFm40rANQX44=1YXEnnB-3eVz1rTR7D8NSmLJzZjg5hmKqZwHg at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi, All,
I ran a NVT simulation for a water sphere with position
restraint. The
TIP4P water model was used. I tried to relax the system at
temperature of
300K. After the simulation, I used gmx energy to cal
the system
temperature and it is around 300K. However, when I tried to
use gmx traj to
extract the temperature from "SOL" group, the temperature is
always half of
that calculated from gmx energy. Is there any difference
between these two
commands? Or is there any other way to determine the
temperature of each
group?
Thank you very much.
Best regards,
Lei Zhao
------------------------------
Message: 2
Date: Tue, 9 Feb 2016 21:24:06 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] wrong number of control atoms (2
iso 3) on
line: 2 3 N -C -CA
Message-ID: <56BA9F46.2070908 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
Please don't reply to the entire digest. If you want
to ask a new question,
just send a new message to the mailing list.
On 2/9/16 5:34 AM, Mehreen Jan wrote:
> gromacs4.5.5
> phosphorylated protein - protein-protein interaction
> phosphate at "SEP" and TPO
> forcefield 43A1p download from gromacs web page
> command:
> pdb2gmx -f protein.pdb -p protein.top -o protein.gro
>
> fatal error:
> error in hdb file ./gromos43A1p.ff/aminoacid.hdb
> wrong number of control atoms (2 iso 3) on line:
> 2 3 N -C -CA
> i read manual but i can't remove error. i did not
get the point how to remove error
>
> HDB file s given:
>
There is no line in this file that would trigger that
error. Make sure you're
looking at, and trying to use, the right files.
-Justin
>
> ABU 1
> 1 1 H N
-C CA
> ACEH 1
> 3 4 HA CA
C O
> AIB 1
> 1 1 H N
-C CA
> ALA 1
> 1 1 H N
-C CA
> ARG 4
> 1 1 H N
-C CA
> 1 1 HE NE
CD CZ
> 2 3 HH1
NH1 CZ NE
> 2 3 HH2
NH2 CZ NE
> ARGN 4
> 1 1 H N
-C CA
> 1 1 HE NE
CD CZ
> 1 2 HH1
NH1 CZ NE
> 2 3 HH2
NH2 CZ NE
> ASN 2
> 1 1 H N
-C CA
> 2 3 HD2
ND2 CG CB
> ASP 1
> 1 1 H N
-C CA
> ASP1 2
> 1 1 H N
-C CA
> 1 2 HD1
OD1 CG CB
> ASPH 2
> 1 1 H N
-C CA
> 1 2 HD2
OD2 CG CB
> BEN 7
> 1 1 H2 C2
C1 C3
> 1 1 H3 C3
C2 C4
> 1 1 H4 C4
C3 C5
> 1 1 H5 C5
C4 C6
> 1 1 H6 C6
C5 C1
> 2 3 H1 N1
C7 C1
> 2 3 H2 N2
C7 C1
> CYS2 1
> 1 1 H N
-C CA
> CYSH 2
> 1 1 H N
-C CA
> 1 2 HG SG
CB CA
> FAD 7
> 2 3 HN6
AN6 AC6 AC5
> 1 2 HO2*
AO2* AC2* AC1*
> 1 2 HO3*
AO3* AC3* AC2*
> 1 2 H4*
O4* C4* C5*
> 1 2 H3*
O3* C3* C4*
> 1 2 H2*
O2* C2* C3*
> 1 2 H3 N3
C4 C4A
> GLN 2
> 1 1 H N
-C CA
> 2 3 HE2
NE2 CD CG
> GLU 1
> 1 1 H N
-C CA
> GLUH 2
> 1 1 H N
-C CA
> 1 2 HE2
OE2 CD CG
> GLY 1
> 1 1 H N
-C CA
> HEME 4
> 1 1 HHA
CHA C1A C4D
> 1 1 HHB
CHB C1B C4A
> 1 1 HHC
CHC C1C C4B
> 1 1 HHD
CHD C1D C4C
> HIS1 2
> 1 1 H N
-C CA
> 1 1 HD1
ND1 CG CE1
> HISA 2
> 1 1 H N
-C CA
> 1 1 HD1
ND1 CG CE1
> HISB 2
> 1 1 H N
-C CA
> 1 1 HE2
NE2 CE1 CD2
> HISH 3
> 1 1 H N
-C CA
> 1 1 HD1
ND1 CG CE1
> 1 1 HE2
NE2 CE1 CD2
> HO4 1
> 3 10 HW OW
> HOH 1
> 2 7 HW OW
> HYP 1
> 1 2 HD1
OD1 CG CB
> ILE 1
> 1 1 H N
-C CA
> LEU 1
> 1 1 H N
-C CA
> LYS 2
> 1 1 H N
-C CA
> 2 4 HZ NZ
CE CD
> LYSH 2
> 1 1 H N
-C CA
> 3 4 HZ NZ
CE CD
> MET 1
> 1 1 H N
-C CA
> NAC 1
> 1 1 H N
-C CA
> NACH 2
> 1 1 H N
-C CA
> 3 4 HA CA
N NH
> NH2 1
> 2 3 H N
-C -CA
> PHE 6
> 1 1 H N
-C CA
> 1 1 HD1
CD1 CG CE1
> 1 1 HD2
CD2 CG CE2
> 1 1 HE1
CE1 CD1 CZ
> 1 1 HE2
CE2 CD2 CZ
> 1 1 HZ CZ
CE1 CE2
> PHEU 1
> 1 1 H N
-C CA
> PHL 7
> 1 1 H N
-C CA
> 1 1 HD1
CD1 CG CE1
> 1 1 HD2
CD2 CG CE2
> 1 1 HE1
CE1 CD1 CZ
> 1 1 HE2
CE2 CD2 CZ
> 1 1 HZ CZ
CE1 CE2
> 1 2 HY OY
CX CA
> SER 2
> 1 1 H N
-C CA
> 1 2 HG OG
CB CA
> TFE 1
> 1 2 H O
CH2 C
> THR 2
> 1 1 H N
-C CA
> 1 2 HG1
OG1 CB CA
> TRP 7
> 1 1 H N
-C CA
> 1 1 HD1
CD1 CG NE1
> 1 1 HE1
NE1 CD1 CE2
> 1 1 HE3
CE3 CD2 CZ3
> 1 1 HZ3
CZ3 CE3 CH2
> 1 1 HH2
CH2 CZ3 CZ2
> 1 1 HZ2
CZ2 CE2 CH2
> TRPU 2
> 1 1 H N
-C CA
> 1 1 HE1
NE1 CD1 CE2
> TYR 6
> 1 1 H N
-C CA
> 1 1 HD1
CD1 CG CE1
> 1 1 HD2
CD2 CG CE2
> 1 1 HE1
CE1 CD1 CZ
> 1 1 HE2
CE2 CD2 CZ
> 1 2 HH OH
CZ CE1
> TYRU 2
> 1 1 H N
-C CA
> 1 2 HH OH
CZ CE1
> VAL 1
> 1 1 H N
-C CA
> SEP 1
> 1 1
H N
-C CA
> TPO 1
> 1 1
H N
-C CA
> PTR 5
> 1 1
H N
-C CA
> 1 1
HD1 CD1
CG CE1
> 1 1
HD2 CD2
CG CE2
> 1 1
HE1 CE1
CD1 CZ
> 1 1
HE2 CE2
CD2 CZ
> SEPH 2
> 1 1
H N
-C CA
> 1 2
H3P O3P
P OG
> TPOH 2
> 1 1
H N
-C CA
> 1 2
H3P O3P
P OG1
> PTRH 6
> 1 1
H N
-C CA
> 1 1
HD1 CD1
CG CE1
> 1 1
HD2 CD2
CG CE2
> 1 1
HE1 CE1
CD1 CZ
> 1 1
HE2 CE2
CD2 CZ
> 1 2
H3P O3P
P OH
>
>
>
> thank you
> mehreen
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
| (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 3
Date: Tue, 9 Feb 2016 21:25:10 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] complex topology file
Message-ID: <56BA9F86.4090808 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 2/9/16 10:54 AM, Sana Saeed wrote:
> hi gmx usersi want to find out absolute binding free
energy of protein ligand
> complex. fisrt i performed docking and selected best
poses and then i made
> topology file of ligand with PRODRGserver. and then
included itp file of
> ligand in Protein topology file (from pdb2gmx) , also
made complex.gro as in
> tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
> . can i use these complex files for MD for absolute
binding free energy? in
> some tutorials the topology file of complex is quite
differently organised.
> please guide me, i am following decoupling and coupling
steps from
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
PRODRG topologies are inaccurate for even simple MD
simulations. Using it for a
free energy calculation is certain to result in junk.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
| (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 4
Date: Tue, 9 Feb 2016 21:25:38 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] difference between gmx energy and
gmx traj
Message-ID: <56BA9FA2.3030906 at vt.edu>
Content-Type: text/plain; charset=windows-1252;
format=flowed
On 2/9/16 5:24 PM, Ray Chao wrote:
> Hi, All,
>
> I ran a NVT simulation for a water sphere with position
restraint. The
> TIP4P water model was used. I tried to relax the system
at temperature of
> 300K. After the simulation, I used gmx energy to
cal the system
> temperature and it is around 300K. However, when I
tried to use gmx traj to
> extract the temperature from "SOL" group, the
temperature is always half of
> that calculated from gmx energy. Is there any
difference between these two
> commands? Or is there any other way to determine the
temperature of each
> group?
>
You need to account for constraints. See the help text
of gmx traj and previous
discussions on this topic in the archive.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
| (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 5
Date: Tue, 9 Feb 2016 21:26:44 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org,
Mahnaz Mirsoltani <mirsoltanim at yahoo.com>
Subject: Re: [gmx-users] add parameter
Message-ID: <56BA9FE4.9070001 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 2/9/16 5:04 PM, Mahnaz Mirsoltani wrote:
> Hi
> I want to add some bond parameters in
ffbonded.itp file, and
> as I read in manual, unit of "kb" is "kj.mol-1.nm-2"
and
> unit of "b0" is "nm". But I have these
quantities with
> "kcal.mol-1.?-2" and "?". How do I
convert these? Is it
Unit transformation is covered in any undergraduate
chemistry or physics text book.
> enough converting of kcal/mol to kj/mol for "kb" and
"?" to
> 'nm" for "b0"?
Yes.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
| (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
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