date:20170519

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

2017-05-19 Thread ZHANG Cheng

Dear Justin,
The command line that got fatal error is:
gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh 
-merge interactive

The command line that works fine is: 
gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge 
interactive
 (just change to another mutant, but the first residue ASP is the same)

I basically interactively assign the protonation state of each chargeable 
residues.

All the screen output is below, quite long:

--
lanselibai@ubuntu:~/Cheng/gromacs/20170517_370K_paper1_mutants/HC_V215W$ gmx 
pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh 
-merge interactive
GROMACS:gmx pdb2gmx, VERSION 5.0.4

GROMACS is written by:
Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par Bjelkmar   
Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch  
Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff  
Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk   
Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers 
Peter Tieleman Christian Wennberg Maarten Wolf   
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, VERSION 5.0.4
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter 
-ignh -merge interactive


Select the Force Field:
>From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15

Using the Oplsaa force field in directory oplsaa.ff

Opening force field file 
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading HC_V215W.pdb...
Read 3342 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Merge chain ending with residue CYS214 (chain id 'L', atom 3258 SG) and chain 
starting with
residue GLU215 (chain id 'H', atom 3263 N) into a single moleculetype (keeping 
termini)? [n/y]
y

Merged chains into joint molecule definitions at 1 places.

There are 1 chains and 0 blocks of water and 442 residues with 3342 atoms

  chain  #res #atoms
  1 'L'   442   3342  

All occupancies are one
Opening force field file 
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 815
Reading residue database... (oplsaa)
Opening force field file 
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 54
Sorting it all out...
Opening force field file 
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
Processing chain 1 'L' (3342 atoms, 442 residues)
Which LYSINE type do you want for residue 24
0. Not protonated (charge 0) (LYS)
1. Protonated (charge +1) (LYSH)

Type a number:1
Which LYSINE type do you want for residue 39
0. Not protonated (charge 0) (LYS)
1. Protonated (charge +1) (ARG)

(here I just interactively assign protonation state)

Identified residue ASP1 as a starting terminus.
Identified residue CYS214 as a ending terminus.
Identified residue

Re: [gmx-users] Error with moleculetype

2017-05-19 Thread Justin Lemkul




On 5/19/17 6:03 PM, Pandya, Akash wrote:

Tried to put it at the end but it still came up with the same error.

Justin, I don't understand what you mean?



If the file has been edited with a non-plain text editor then you can have 
malformed return characters.  Make sure you only ever edit files with vim, 
emacs, etc. and if you're using any Windows-specific editors, process files with 
dos2unix.


-Justin


Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 19 May 2017 22:35
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error with moleculetype



On 5/19/17 5:33 PM, Mark Abraham wrote:

Hi,

Ok. Maybe it needs to be last in the molecules?



Or perhaps the error points to a malformed line ending that causes genion to 
choke when updating the topology.

-Justin


Mark

On Fri, 19 May 2017 23:19 Pandya, Akash  wrote:


It was the genion command. Here is the message.

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of
file 'topol.top'

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
Abraham
Sent: 19 May 2017 21:26
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Error with moleculetype

Hi,

I don't think grompp can issue that message. What was the message you
copied and pasted from your terminal?

Mark

On Fri, 19 May 2017 18:49 Pandya, Akash  wrote:


Hi all,

I have received an error message shown below.

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of
file 'topol.top'

For more information and tips for troubleshooting, please check the
GROMACS website at http://www.gromacs.org/Documentation/Errors

I don't understand what's wrong with my topol.top file. I have
included the following before the [ molecules ] section.

[ moleculetype ]
; Name
SOL 1

My [ molecules ] section looks like this:

[ molecules ]
; Compound#mols
Protein_chain_H 1
SOL 73337
Citrate29
GLY   984


I have read the documentation and still don't understand. Please can
you advise me on what to do?

Many thanks,
Akash

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--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

2017-05-19 Thread Justin Lemkul




On 5/19/17 6:31 PM, ZHANG Cheng wrote:

Dear Justin,
I replied the thread already, but it is waiting for approval due to large email 
content. Could you please approve it?



I have no control over that.  If it's too much for an email (normally pdb2gmx 
output is fine) then upload to e.g. pastebin and provide the URL.


-Justin


Cheng

---Original---
From: "ZHANG Cheng"<272699...@qq.com>
Date: 2017/5/19 22:37:52
To: "gromacs.org_gmx-users";
Cc: "QQ"<272699...@qq.com>;
Subject: pdb2gmx: Atom N used in the topology not found in the input (PDB) file


Dear Gromacs,
I got this fatal error after running "pdb2gmx":


Fatal error:
Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.



However, the residue 1 in the PDB is:


ATOM  1  N   ASP L   1  24.330  14.711  -3.854  1.00  0.00   N
ATOM  2  CA  ASP L   1  25.669  15.093  -3.310  1.00  0.00   C
ATOM  3  C   ASP L   1  25.766  14.899  -1.791  1.00  0.00   C
ATOM  4  O   ASP L   1  26.581  14.101  -1.318  1.00  0.00   O
ATOM  5  CB  ASP L   1  25.989  16.552  -3.646  1.00  0.00   C
ATOM  6  CG  ASP L   1  26.260  16.773  -5.128  1.00  0.00   C
ATOM  7  OD1 ASP L   1  26.489  15.809  -5.821  1.00  0.00   O
ATOM  8  OD2 ASP L   1  26.236  17.903  -5.554  1.00  0.00   O
ATOM  9 1H   ASP L   1  24.318  14.855  -4.844  1.00  0.00   H
ATOM 10 2H   ASP L   1  24.152  13.747  -3.656  1.00  0.00   H
ATOM 11 3H   ASP L   1  23.623  15.275  -3.427  1.00  0.00   H
ATOM 12  HA  ASP L   1  26.425  14.456  -3.771  1.00  0.00   H
ATOM 13 1HB  ASP L   1  25.154  17.186  -3.346  1.00  0.00   H
ATOM 14 2HB  ASP L   1  26.864  16.873  -3.080  1.00  0.00   H



You can see that the first atom is just atom N, not missing. Can I ask why I 
still got this error?


Another mutant file of the protein works totally fine for pdb2gmx. Its 1st 
residue ASP is the below, I could not see any big difference except slight 
difference in the coordinates.


ATOM  1  N   ASP L   1  24.330  14.711  -3.854  1.00  0.00   N
ATOM  2  CA  ASP L   1  25.669  15.093  -3.310  1.00  0.00   C
ATOM  3  C   ASP L   1  25.766  14.899  -1.791  1.00  0.00   C
ATOM  4  O   ASP L   1  26.586  14.106  -1.317  1.00  0.00   O
ATOM  5  CB  ASP L   1  25.989  16.552  -3.646  1.00  0.00   C
ATOM  6  CG  ASP L   1  26.260  16.773  -5.128  1.00  0.00   C
ATOM  7  OD1 ASP L   1  26.489  15.810  -5.821  1.00  0.00   O
ATOM  8  OD2 ASP L   1  26.235  17.904  -5.554  1.00  0.00   O
ATOM  9 1H   ASP L   1  24.318  14.855  -4.844  1.00  0.00   H
ATOM 10 2H   ASP L   1  24.152  13.747  -3.656  1.00  0.00   H
ATOM 11 3H   ASP L   1  23.623  15.275  -3.427  1.00  0.00   H
ATOM 12  HA  ASP L   1  26.425  14.456  -3.771  1.00  0.00   H
ATOM 13 1HB  ASP L   1  25.154  17.186  -3.345  1.00  0.00   H
ATOM 14 2HB  ASP L   1  26.864  16.872  -3.080  1.00  0.00   H


Thank you.


Yours sincerely
Cheng



--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

2017-05-19 Thread ZHANG Cheng

Dear Justin,
I replied the thread already, but it is waiting for approval due to large email 
content. Could you please approve it?

Cheng

---Original---
From: "ZHANG Cheng"<272699...@qq.com>
Date: 2017/5/19 22:37:52
To: "gromacs.org_gmx-users";
Cc: "QQ"<272699...@qq.com>;
Subject: pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Dear Gromacs,
I got this fatal error after running "pdb2gmx":

Fatal error:
Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

However, the residue 1 in the PDB is:

ATOM  1  N   ASP L   1  24.330  14.711  -3.854  1.00  0.00   N  
ATOM  2  CA  ASP L   1  25.669  15.093  -3.310  1.00  0.00   C  
ATOM  3  C   ASP L   1  25.766  14.899  -1.791  1.00  0.00   C  
ATOM  4  O   ASP L   1  26.581  14.101  -1.318  1.00  0.00   O  
ATOM  5  CB  ASP L   1  25.989  16.552  -3.646  1.00  0.00   C  
ATOM  6  CG  ASP L   1  26.260  16.773  -5.128  1.00  0.00   C  
ATOM  7  OD1 ASP L   1  26.489  15.809  -5.821  1.00  0.00   O  
ATOM  8  OD2 ASP L   1  26.236  17.903  -5.554  1.00  0.00   O  
ATOM  9 1H   ASP L   1  24.318  14.855  -4.844  1.00  0.00   H  
ATOM 10 2H   ASP L   1  24.152  13.747  -3.656  1.00  0.00   H  
ATOM 11 3H   ASP L   1  23.623  15.275  -3.427  1.00  0.00   H  
ATOM 12  HA  ASP L   1  26.425  14.456  -3.771  1.00  0.00   H  
ATOM 13 1HB  ASP L   1  25.154  17.186  -3.346  1.00  0.00   H  
ATOM 14 2HB  ASP L   1  26.864  16.873  -3.080  1.00  0.00   H 

You can see that the first atom is just atom N, not missing. Can I ask why I 
still got this error?

Another mutant file of the protein works totally fine for pdb2gmx. Its 1st 
residue ASP is the below, I could not see any big difference except slight 
difference in the coordinates.

ATOM  1  N   ASP L   1  24.330  14.711  -3.854  1.00  0.00   N  
ATOM  2  CA  ASP L   1  25.669  15.093  -3.310  1.00  0.00   C  
ATOM  3  C   ASP L   1  25.766  14.899  -1.791  1.00  0.00   C  
ATOM  4  O   ASP L   1  26.586  14.106  -1.317  1.00  0.00   O  
ATOM  5  CB  ASP L   1  25.989  16.552  -3.646  1.00  0.00   C  
ATOM  6  CG  ASP L   1  26.260  16.773  -5.128  1.00  0.00   C  
ATOM  7  OD1 ASP L   1  26.489  15.810  -5.821  1.00  0.00   O  
ATOM  8  OD2 ASP L   1  26.235  17.904  -5.554  1.00  0.00   O  
ATOM  9 1H   ASP L   1  24.318  14.855  -4.844  1.00  0.00   H  
ATOM 10 2H   ASP L   1  24.152  13.747  -3.656  1.00  0.00   H  
ATOM 11 3H   ASP L   1  23.623  15.275  -3.427  1.00  0.00   H  
ATOM 12  HA  ASP L   1  26.425  14.456  -3.771  1.00  0.00   H  
ATOM 13 1HB  ASP L   1  25.154  17.186  -3.345  1.00  0.00   H  
ATOM 14 2HB  ASP L   1  26.864  16.872  -3.080  1.00  0.00   H

Thank you.

Yours sincerely
Cheng
-- 
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Re: [gmx-users] Error with moleculetype

2017-05-19 Thread Pandya, Akash

Tried to put it at the end but it still came up with the same error. 

Justin, I don't understand what you mean?

Akash

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 19 May 2017 22:35
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error with moleculetype



On 5/19/17 5:33 PM, Mark Abraham wrote:
> Hi,
>
> Ok. Maybe it needs to be last in the molecules?
>

Or perhaps the error points to a malformed line ending that causes genion to 
choke when updating the topology.

-Justin

> Mark
>
> On Fri, 19 May 2017 23:19 Pandya, Akash  wrote:
>
>> It was the genion command. Here is the message.
>>
>> Fatal error:
>> No line with moleculetype 'SOL' found the [ molecules ] section of 
>> file 'topol.top'
>>
>> -Original Message-
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
>> Abraham
>> Sent: 19 May 2017 21:26
>> To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: Re: [gmx-users] Error with moleculetype
>>
>> Hi,
>>
>> I don't think grompp can issue that message. What was the message you 
>> copied and pasted from your terminal?
>>
>> Mark
>>
>> On Fri, 19 May 2017 18:49 Pandya, Akash  wrote:
>>
>>> Hi all,
>>>
>>> I have received an error message shown below.
>>>
>>> Fatal error:
>>> No line with moleculetype 'SOL' found the [ molecules ] section of 
>>> file 'topol.top'
>>>
>>> For more information and tips for troubleshooting, please check the 
>>> GROMACS website at http://www.gromacs.org/Documentation/Errors
>>>
>>> I don't understand what's wrong with my topol.top file. I have 
>>> included the following before the [ molecules ] section.
>>>
>>> [ moleculetype ]
>>> ; Name
>>> SOL 1
>>>
>>> My [ molecules ] section looks like this:
>>>
>>> [ molecules ]
>>> ; Compound#mols
>>> Protein_chain_H 1
>>> SOL 73337
>>> Citrate29
>>> GLY   984
>>>
>>>
>>> I have read the documentation and still don't understand. Please can 
>>> you advise me on what to do?
>>>
>>> Many thanks,
>>> Akash
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
>>> posting!
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>>> or send a mail to gmx-users-requ...@gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>

--
==

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

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Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

2017-05-19 Thread Justin Lemkul




On 5/19/17 5:37 PM, ZHANG Cheng wrote:

Dear Gromacs,
I got this fatal error after running "pdb2gmx":



Please provide your exact command and full screen output.  There's a lot of 
relevant information there, because pdb2gmx is doing a lot of complex things.


-Justin



Fatal error:
Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.



However, the residue 1 in the PDB is:


ATOM  1  N   ASP L   1  24.330  14.711  -3.854  1.00  0.00   N
ATOM  2  CA  ASP L   1  25.669  15.093  -3.310  1.00  0.00   C
ATOM  3  C   ASP L   1  25.766  14.899  -1.791  1.00  0.00   C
ATOM  4  O   ASP L   1  26.581  14.101  -1.318  1.00  0.00   O
ATOM  5  CB  ASP L   1  25.989  16.552  -3.646  1.00  0.00   C
ATOM  6  CG  ASP L   1  26.260  16.773  -5.128  1.00  0.00   C
ATOM  7  OD1 ASP L   1  26.489  15.809  -5.821  1.00  0.00   O
ATOM  8  OD2 ASP L   1  26.236  17.903  -5.554  1.00  0.00   O
ATOM  9 1H   ASP L   1  24.318  14.855  -4.844  1.00  0.00   H
ATOM 10 2H   ASP L   1  24.152  13.747  -3.656  1.00  0.00   H
ATOM 11 3H   ASP L   1  23.623  15.275  -3.427  1.00  0.00   H
ATOM 12  HA  ASP L   1  26.425  14.456  -3.771  1.00  0.00   H
ATOM 13 1HB  ASP L   1  25.154  17.186  -3.346  1.00  0.00   H
ATOM 14 2HB  ASP L   1  26.864  16.873  -3.080  1.00  0.00   H



You can see that the first atom is just atom N, not missing. Can I ask why I 
still got this error?


Another mutant file of the protein works totally fine for pdb2gmx. Its 1st 
residue ASP is the below, I could not see any big difference except slight 
difference in the coordinates.


ATOM  1  N   ASP L   1  24.330  14.711  -3.854  1.00  0.00   N
ATOM  2  CA  ASP L   1  25.669  15.093  -3.310  1.00  0.00   C
ATOM  3  C   ASP L   1  25.766  14.899  -1.791  1.00  0.00   C
ATOM  4  O   ASP L   1  26.586  14.106  -1.317  1.00  0.00   O
ATOM  5  CB  ASP L   1  25.989  16.552  -3.646  1.00  0.00   C
ATOM  6  CG  ASP L   1  26.260  16.773  -5.128  1.00  0.00   C
ATOM  7  OD1 ASP L   1  26.489  15.810  -5.821  1.00  0.00   O
ATOM  8  OD2 ASP L   1  26.235  17.904  -5.554  1.00  0.00   O
ATOM  9 1H   ASP L   1  24.318  14.855  -4.844  1.00  0.00   H
ATOM 10 2H   ASP L   1  24.152  13.747  -3.656  1.00  0.00   H
ATOM 11 3H   ASP L   1  23.623  15.275  -3.427  1.00  0.00   H
ATOM 12  HA  ASP L   1  26.425  14.456  -3.771  1.00  0.00   H
ATOM 13 1HB  ASP L   1  25.154  17.186  -3.345  1.00  0.00   H
ATOM 14 2HB  ASP L   1  26.864  16.872  -3.080  1.00  0.00   H


Thank you.


Yours sincerely
Cheng



--
==

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
20 Penn St.
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Re: [gmx-users] Need to confirm parameters.

2017-05-19 Thread Justin Lemkul




On 5/19/17 8:22 AM, Sailesh Bataju wrote:

Hi Sir,

You mean like choosing OPLS forcefield for all-atom model would be moer
appropriate for me?



At minimum, some all-atom force field, because whatever you were doing before 
has no relationship to GROMOS and is unlikely to succeed.


Isobutane is just the valine side chain, so that's certainly a model compound in 
existing force fields and should have parameters published and validated for any 
of the major all-atom force fields.  I know it's in CHARMM, and certainly others.


-Justin


Thank you.

On Fri, May 19, 2017 at 5:15 PM, Sailesh Bataju  wrote:


Hi Sir/Ma'am,

I've finally created parameter file of isobutane using gromos54a7
forcefield for all-atom model. Some of the parameters for bond angle
parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
file in the relevant forcefield, instead I used FTFE  -  CTFE  -  FTFE and
CLChl  - CChl  - CLChl respectively which i found it in the sample of the
file generated by https://atb.uq.edu.au/ website. Somehow luckily found
corresponding bond angle approximately equivalent to the experimental data
observed but didn't find the bond angle constant in experimental data.
Therefore I'm not sure if I can trust the parameter selected.

I need your advice to help me decide to go further.
Thank you very much.

--
Self-reliant is the great potential for success.







--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

2017-05-19 Thread ZHANG Cheng

Dear Gromacs,
I got this fatal error after running "pdb2gmx":


Fatal error:
Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.



However, the residue 1 in the PDB is:


ATOM  1  N   ASP L   1  24.330  14.711  -3.854  1.00  0.00   N  
ATOM  2  CA  ASP L   1  25.669  15.093  -3.310  1.00  0.00   C  
ATOM  3  C   ASP L   1  25.766  14.899  -1.791  1.00  0.00   C  
ATOM  4  O   ASP L   1  26.581  14.101  -1.318  1.00  0.00   O  
ATOM  5  CB  ASP L   1  25.989  16.552  -3.646  1.00  0.00   C  
ATOM  6  CG  ASP L   1  26.260  16.773  -5.128  1.00  0.00   C  
ATOM  7  OD1 ASP L   1  26.489  15.809  -5.821  1.00  0.00   O  
ATOM  8  OD2 ASP L   1  26.236  17.903  -5.554  1.00  0.00   O  
ATOM  9 1H   ASP L   1  24.318  14.855  -4.844  1.00  0.00   H  
ATOM 10 2H   ASP L   1  24.152  13.747  -3.656  1.00  0.00   H  
ATOM 11 3H   ASP L   1  23.623  15.275  -3.427  1.00  0.00   H  
ATOM 12  HA  ASP L   1  26.425  14.456  -3.771  1.00  0.00   H  
ATOM 13 1HB  ASP L   1  25.154  17.186  -3.346  1.00  0.00   H  
ATOM 14 2HB  ASP L   1  26.864  16.873  -3.080  1.00  0.00   H 



You can see that the first atom is just atom N, not missing. Can I ask why I 
still got this error?


Another mutant file of the protein works totally fine for pdb2gmx. Its 1st 
residue ASP is the below, I could not see any big difference except slight 
difference in the coordinates.


ATOM  1  N   ASP L   1  24.330  14.711  -3.854  1.00  0.00   N  
ATOM  2  CA  ASP L   1  25.669  15.093  -3.310  1.00  0.00   C  
ATOM  3  C   ASP L   1  25.766  14.899  -1.791  1.00  0.00   C  
ATOM  4  O   ASP L   1  26.586  14.106  -1.317  1.00  0.00   O  
ATOM  5  CB  ASP L   1  25.989  16.552  -3.646  1.00  0.00   C  
ATOM  6  CG  ASP L   1  26.260  16.773  -5.128  1.00  0.00   C  
ATOM  7  OD1 ASP L   1  26.489  15.810  -5.821  1.00  0.00   O  
ATOM  8  OD2 ASP L   1  26.235  17.904  -5.554  1.00  0.00   O  
ATOM  9 1H   ASP L   1  24.318  14.855  -4.844  1.00  0.00   H  
ATOM 10 2H   ASP L   1  24.152  13.747  -3.656  1.00  0.00   H  
ATOM 11 3H   ASP L   1  23.623  15.275  -3.427  1.00  0.00   H  
ATOM 12  HA  ASP L   1  26.425  14.456  -3.771  1.00  0.00   H  
ATOM 13 1HB  ASP L   1  25.154  17.186  -3.345  1.00  0.00   H  
ATOM 14 2HB  ASP L   1  26.864  16.872  -3.080  1.00  0.00   H


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

2017-05-19 Thread Justin Lemkul




On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote:

First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file 
I found different linkages for beta-glucose, but non for alpha-glucose.
I am trying to make a simple chain with 1->4 linkages like below:

alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.



Linkages are not specific to the sugar; most are totally generic.  A few 
comments suggest specific usage and may be corner cases, but your patches will 
be among 14aa, 14ab, 14ba, 14bb.




Then, I might need to branch them with1->6 linkage.


Also totally possible.


I tried Glycan Reader, but itstill crashes.



Uploading a correctly named PDB file should work in Glycan Reader or the Quick 
MD Simulator, but "still crashes" is not diagnostic of anything.  Specific help 
with CHARMM-GUI should be brought to their attention, though.


-Justin


MH



Thanks Justin.
I have tried the CHARMM-GUI but it crashed. I might need to modify the order of 
the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I have 
downloaded the “toppar_c36_feb16” but I did not find a manual on how to apply 
them (any suggestions?), so it did not go far.


What you need to do depends on linkages.  There are patches (PRES in CHARMM 
.rtf files) that tell you how each residue is manipulated in the case of a 
patch; refer to the CHARMM documentation online for specifics.  The file you'll 
need is top_all36_carb.rtf.

Otherwise, use the force field files as a template to rename your input 
structure so CHARMM-GUI can process it.  This is probably the much faster route.

-Justin


I'll play with these two, and I'll be back.
MH

On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:



On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote:

Hi,

I am trying to run simulations on alpha-D-glucose polymers. I have done these 
simulations using AMBER and I am wondering if it is possible to run them 
employing CHARMM36 in GROMACS, as well?
It seams that CHARMM36 in GROMACS has only implemented monomers of 
alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the 
GROMACS?



Sure, you can treat it like any polymer, but you'll have to create the internal 
monomer residues yourself from the patches in the original CHARMM force field 
files.

Or try CHARMM-GUI; it should handle what you need and give you all the 
necessary GROMACS inputs.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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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

jalem...@outerbanks.umaryland.edu  | 
(410) 706-7441
http://mackerell.umaryland.edu/~jalemkul 


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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

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Re: [gmx-users] Error with moleculetype

2017-05-19 Thread Justin Lemkul




On 5/19/17 5:33 PM, Mark Abraham wrote:

Hi,

Ok. Maybe it needs to be last in the molecules?



Or perhaps the error points to a malformed line ending that causes genion to 
choke when updating the topology.


-Justin


Mark

On Fri, 19 May 2017 23:19 Pandya, Akash  wrote:


It was the genion command. Here is the message.

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'topol.top'

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
Abraham
Sent: 19 May 2017 21:26
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Error with moleculetype

Hi,

I don't think grompp can issue that message. What was the message you
copied and pasted from your terminal?

Mark

On Fri, 19 May 2017 18:49 Pandya, Akash  wrote:


Hi all,

I have received an error message shown below.

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of
file 'topol.top'

For more information and tips for troubleshooting, please check the
GROMACS website at http://www.gromacs.org/Documentation/Errors

I don't understand what's wrong with my topol.top file. I have
included the following before the [ molecules ] section.

[ moleculetype ]
; Name
SOL 1

My [ molecules ] section looks like this:

[ molecules ]
; Compound#mols
Protein_chain_H 1
SOL 73337
Citrate29
GLY   984


I have read the documentation and still don't understand. Please can
you advise me on what to do?

Many thanks,
Akash

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==

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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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] Error with moleculetype

2017-05-19 Thread Mark Abraham

Hi,

Ok. Maybe it needs to be last in the molecules?

Mark

On Fri, 19 May 2017 23:19 Pandya, Akash  wrote:

> It was the genion command. Here is the message.
>
> Fatal error:
> No line with moleculetype 'SOL' found the [ molecules ] section of file
> 'topol.top'
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: 19 May 2017 21:26
> To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Error with moleculetype
>
> Hi,
>
> I don't think grompp can issue that message. What was the message you
> copied and pasted from your terminal?
>
> Mark
>
> On Fri, 19 May 2017 18:49 Pandya, Akash  wrote:
>
> > Hi all,
> >
> > I have received an error message shown below.
> >
> > Fatal error:
> > No line with moleculetype 'SOL' found the [ molecules ] section of
> > file 'topol.top'
> >
> > For more information and tips for troubleshooting, please check the
> > GROMACS website at http://www.gromacs.org/Documentation/Errors
> >
> > I don't understand what's wrong with my topol.top file. I have
> > included the following before the [ molecules ] section.
> >
> > [ moleculetype ]
> > ; Name
> > SOL 1
> >
> > My [ molecules ] section looks like this:
> >
> > [ molecules ]
> > ; Compound#mols
> > Protein_chain_H 1
> > SOL 73337
> > Citrate29
> > GLY   984
> >
> >
> > I have read the documentation and still don't understand. Please can
> > you advise me on what to do?
> >
> > Many thanks,
> > Akash
> >
> > --
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Re: [gmx-users] Error with moleculetype

2017-05-19 Thread Pandya, Akash

It was the genion command. Here is the message.

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'topol.top'

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: 19 May 2017 21:26
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Error with moleculetype

Hi,

I don't think grompp can issue that message. What was the message you copied 
and pasted from your terminal?

Mark

On Fri, 19 May 2017 18:49 Pandya, Akash  wrote:

> Hi all,
>
> I have received an error message shown below.
>
> Fatal error:
> No line with moleculetype 'SOL' found the [ molecules ] section of 
> file 'topol.top'
>
> For more information and tips for troubleshooting, please check the 
> GROMACS website at http://www.gromacs.org/Documentation/Errors
>
> I don't understand what's wrong with my topol.top file. I have 
> included the following before the [ molecules ] section.
>
> [ moleculetype ]
> ; Name
> SOL 1
>
> My [ molecules ] section looks like this:
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_H 1
> SOL 73337
> Citrate29
> GLY   984
>
>
> I have read the documentation and still don't understand. Please can 
> you advise me on what to do?
>
> Many thanks,
> Akash
>
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Re: [gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

2017-05-19 Thread Mark Abraham

Hi,

Historically that was how things were done. Nobody thinks it is a good idea
any more. Use the Verlet scheme plus the recommendations for CHARMM
forcefields in GROMACS and you'll be fine - charge groups are removed
perforce.

Mark

On Fri, 19 May 2017 18:44 Dawid das  wrote:

> Dear  Gromacs Users,
>
> I am a bit confused whether I shouldn't use charge
> group-based cut-off for electrostatics when using CHARMM22.
> If I shouldn't use it, what is the purpose of specification of charge
> groups in
> original CHARMM files?
>
> Best wishes,
> Dawid
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[gmx-users] Error with moleculetype

2017-05-19 Thread Pandya, Akash

Hi all,

I have received an error message shown below.

Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
'topol.top'

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I don't understand what's wrong with my topol.top file. I have included the 
following before the [ molecules ] section.

[ moleculetype ]
; Name
SOL 1

My [ molecules ] section looks like this:

[ molecules ]
; Compound#mols
Protein_chain_H 1
SOL 73337
Citrate29
GLY   984


I have read the documentation and still don't understand. Please can you advise 
me on what to do?

Many thanks,
Akash

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[gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

2017-05-19 Thread Dawid das

Dear  Gromacs Users,

I am a bit confused whether I shouldn't use charge
group-based cut-off for electrostatics when using CHARMM22.
If I shouldn't use it, what is the purpose of specification of charge
groups in
original CHARMM files?

Best wishes,
Dawid
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[gmx-users] Nonequilibrium simulations

2017-05-19 Thread jwillcox

Hello,

I am running non-equilibrium simulations using the "acc-groups" command
and the Nose-Hoover thermostat.  I just wanted to confirm that in Gromacs
code this additional acceleration is not considered to contribute to the
temperature when velocities are adjusted.

Thank you!

Jon

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Re: [gmx-users] Graphene modeling

2017-05-19 Thread ‪Mohammad Roostaie‬ ‪

Hi Justin,
Thank you very much. It is Ok now.
Best,Mohammad

  From: Justin Lemkul 
 To: Discussion list for GROMACS users  
 Sent: Tuesday, 16 May 2017, 18:34:14
 Subject: Re: [gmx-users] Graphene modeling
   


On 5/16/17 7:31 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> In addition, I used this command "gmx x2top -f g.gro -o g.top -ff cnt_oplsaa
> -name CNT -noparam" and I got this error:
>
> Opening force field file ./cnt_oplsaa.ff/atomnames2types.n2t
> There are 6 name to type translations in file ./cnt_oplsaa.ff
> Generating bonds from distances...
> atom 46
> There are 1 different atom types in your sample
> Generating angles and dihedrals from bonds...
> Segmentation fault
>

Are you using the latest version of GROMACS?  There was an x2top seg fault 
fixed 
a few versions ago so using 2016.3 may be necessary here.

-Justin

> Best
> Mohammad
>
>
> 
> *From:* ‪Mohammad Roostaie‬ ‪ 
> *To:* Justin Lemkul ; gmx-us...@gromacs.org
> *Sent:* Tuesday, 16 May 2017, 13:59:29
> *Subject:* Re: [gmx-users] Graphene modeling
>
> Thank you Justin,
>
> Actually, I want to simulate a small box of water with graphene and protein. 
> You
> mean that I should just build and put the .n2t file in the directory where I
> want to run the system, and no other files are required or should not be 
> changed.
>
> I used the files specified in this
> link: http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
> 
>
> For example, for .n2t file:
>
> |; Oplsaa-based n2t for carbon-based structures such as CNTs and graphenes ;
> Andrea Minoia H HJ 0.00 1.008 1 C 0.109 ;Hydrogen C CJ 0.00 12.011 3 C 0.142 H
> 0.109 H 0.109 ;Periferic C C CJ 0.00 12.011 3 C 0.142 C 0.142 H 0.108 
> ;Periferic
> C C CJ 0.00 12.011 1 C 0.142 ;Internal/periodic C C CJ 0.00 12.011 2 C 0.142 C
> 0.142 ;Internal/periodic C C CJ 0.00 12.011 3 C 0.142 C 0.142 C 0.142
> ;Internal/periodic C|
>
>
> Thanks,
> Mohammad
> 
> *From:* Justin Lemkul 
> *To:* gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪ 
> *Sent:* Monday, 15 May 2017, 16:45:19
> *Subject:* Re: [gmx-users] Graphene modeling
>
>
>
> On 5/14/17 9:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>> Hi GROMACS users,
>>
>>
>>
>> I want to model a graphene sheet. I used the instruction stated in link
> http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube.
> I put the
> cnt_oplsaa.ff folder in the directory where I want to run the rest of the 
> work.
> Also, I rename the residues of the graphene to “CJ” and the atoms to “C”. but,
> when I want to use “gmx x2top”, I get the error that says it cannot find any
> forcefield type for the atoms. Can you please help me to figure this out?
>
>>
>
> Since all you have are C atoms, this should require only a one-line .n2t file
> (or addition to an existing one) that specifies the proper equilibrium bond
> length for C-C in your structure.  Without seeing your .n2t file and the x2top
> screen output, there's nothing to suggest other than your .n2t file is somehow
> inadequate for what you're trying to do.
>
> -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
>
> jalem...@outerbanks.umaryland.edu  |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==
>
>
>
>

-- 
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

2017-05-19 Thread Mohammad Hassan Khatami

First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file 
I found different linkages for beta-glucose, but non for alpha-glucose.
I am trying to make a simple chain with 1->4 linkages like below:

alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.


Then, I might need to branch them with1->6 linkage.
I tried Glycan Reader, but it still crashes.

MH
> 
>> Thanks Justin.
>> I have tried the CHARMM-GUI but it crashed. I might need to modify the order 
>> of the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I 
>> have downloaded the “toppar_c36_feb16” but I did not find a manual on how to 
>> apply them (any suggestions?), so it did not go far.
> 
> What you need to do depends on linkages.  There are patches (PRES in CHARMM 
> .rtf files) that tell you how each residue is manipulated in the case of a 
> patch; refer to the CHARMM documentation online for specifics.  The file 
> you'll need is top_all36_carb.rtf.
> 
> Otherwise, use the force field files as a template to rename your input 
> structure so CHARMM-GUI can process it.  This is probably the much faster 
> route.
> 
> -Justin
> 
>> I'll play with these two, and I'll be back.
>> MH
>>> On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote:
 Hi,
 
 I am trying to run simulations on alpha-D-glucose polymers. I have done 
 these simulations using AMBER and I am wondering if it is possible to run 
 them employing CHARMM36 in GROMACS, as well?
 It seams that CHARMM36 in GROMACS has only implemented monomers of 
 alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer 
 to the GROMACS?
 
>>> 
>>> Sure, you can treat it like any polymer, but you'll have to create the 
>>> internal monomer residues yourself from the patches in the original CHARMM 
>>> force field files.
>>> 
>>> Or try CHARMM-GUI; it should handle what you need and give you all the 
>>> necessary GROMACS inputs.
>>> 
>>> -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
>>> 
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>> 
>>> ==
>>> --
>>> Gromacs Users mailing list
>>> 
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>>> a mail to gmx-users-requ...@gromacs.org.
>> 
> 
> -- 
> ==
> 
> 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
> 
> jalem...@outerbanks.umaryland.edu  
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> 
> 
> ==
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Re: [gmx-users] Need to confirm parameters.

2017-05-19 Thread Sailesh Bataju

Hi Sir,

You mean like choosing OPLS forcefield for all-atom model would be moer
appropriate for me?

Thank you.

On Fri, May 19, 2017 at 5:15 PM, Sailesh Bataju  wrote:

> Hi Sir/Ma'am,
>
> I've finally created parameter file of isobutane using gromos54a7
> forcefield for all-atom model. Some of the parameters for bond angle
> parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
> file in the relevant forcefield, instead I used FTFE  -  CTFE  -  FTFE and
> CLChl  - CChl  - CLChl respectively which i found it in the sample of the
> file generated by https://atb.uq.edu.au/ website. Somehow luckily found
> corresponding bond angle approximately equivalent to the experimental data
> observed but didn't find the bond angle constant in experimental data.
> Therefore I'm not sure if I can trust the parameter selected.
>
> I need your advice to help me decide to go further.
> Thank you very much.
>
> --
> Self-reliant is the great potential for success.
>

-- 
Self-reliant is the great potential for success.
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[gmx-users] Regarding sampling convergence

2017-05-19 Thread Subhomoi Borkotoky

Dear users,

I have a 100 ns simulation trajectory and I have generated FEL (free energy
landscape) with it to extract a minimum energy conformation of my protein.

How can I show sampling convergence of FEL  in gromacs? Do I have to split
the trajectory (say at every 20ns) and generate FELs from them to compare?

-- 
Yours Sincerely,
--
SUBHOMOI BORKOTOKY,
Centre for Bioinformatics
Pondicherry University
Pondicherry,INDIA.

Alternate Email: subho...@mails.bicpu.edu.in

https://scholar.google.co.in/citations?user=bJz7GokJ=en
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Re: [gmx-users] ligand moving out during umbrella sampling

2017-05-19 Thread Justin Lemkul




On 5/19/17 5:56 AM, abhisek Mondal wrote:

On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:




On 5/17/17 8:55 AM, abhisek Mondal wrote:


This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in the
following
link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

However, I'm facing a problem. Due to the withdrawal of the position
restrain of protein. The protein and ligand (together) is moving around
the
box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
than 0.49 times the box size (10.646989)" error.

As per the video I have uploaded, if I assume this approach worked, then
how can I avoid this error ? Is  there any way to make sure the
protein-ligand remains in the middle of the box (or nearby). I have taken
pretty large box compared to the protein structure from the beginning.

Please suggest me a way out.



Use a larger box or use direction-periodic geometry.



 For the sake of computational power I'm leaning towards direction-periodic
geometry. However, from the mailing list entries I found out that pressure
coupling should not be used for this kind of geometry setup.
NVT coupling with no velocity generation is what I'm opting for. There are
a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
Would you please suggest if the code (
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0) looks
sensible ?

Eagerly waiting for your opinion.



Try it and see what happens.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

2017-05-19 Thread Justin Lemkul




On 5/18/17 6:35 PM, Mohammad Hassan Khatami wrote:

Thanks Justin.
I have tried the CHARMM-GUI but it crashed. I might need to modify the order of 
the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I have 
downloaded the “toppar_c36_feb16” but I did not find a manual on how to apply 
them (any suggestions?), so it did not go far.


What you need to do depends on linkages.  There are patches (PRES in CHARMM .rtf 
files) that tell you how each residue is manipulated in the case of a patch; 
refer to the CHARMM documentation online for specifics.  The file you'll need is 
top_all36_carb.rtf.


Otherwise, use the force field files as a template to rename your input 
structure so CHARMM-GUI can process it.  This is probably the much faster route.


-Justin


I'll play with these two, and I'll be back.
MH

On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:



On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote:

Hi,

I am trying to run simulations on alpha-D-glucose polymers. I have done these 
simulations using AMBER and I am wondering if it is possible to run them 
employing CHARMM36 in GROMACS, as well?
It seams that CHARMM36 in GROMACS has only implemented monomers of 
alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the 
GROMACS?



Sure, you can treat it like any polymer, but you'll have to create the internal 
monomer residues yourself from the patches in the original CHARMM force field 
files.

Or try CHARMM-GUI; it should handle what you need and give you all the 
necessary GROMACS inputs.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Need to confirm parameters.

2017-05-19 Thread Justin Lemkul




On 5/19/17 7:30 AM, Sailesh Bataju wrote:

Hi Sir/Ma'am,

I've finally created parameter file of isobutane using gromos54a7
forcefield for all-atom model. Some of the parameters for bond angle
parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
file in the relevant forcefield, instead I used FTFE  -  CTFE  -  FTFE and
CLChl  - CChl  - CLChl respectively which i found it in the sample of the
file generated by https://atb.uq.edu.au/ website. Somehow luckily found
corresponding bond angle approximately equivalent to the experimental data
observed but didn't find the bond angle constant in experimental data.
Therefore I'm not sure if I can trust the parameter selected.



GROMOS force fields are united-atom so isobutane will have no H atoms.  Use a 
sensible all-atom model as your starting point, because any of them will have 
the actual parameters you need rather than trying to rely on halogens as analogs 
of H atoms.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Need to confirm parameters.

2017-05-19 Thread Sailesh Bataju

Hi Sir/Ma'am,

I've finally created parameter file of isobutane using gromos54a7
forcefield for all-atom model. Some of the parameters for bond angle
parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
file in the relevant forcefield, instead I used FTFE  -  CTFE  -  FTFE and
CLChl  - CChl  - CLChl respectively which i found it in the sample of the
file generated by https://atb.uq.edu.au/ website. Somehow luckily found
corresponding bond angle approximately equivalent to the experimental data
observed but didn't find the bond angle constant in experimental data.
Therefore I'm not sure if I can trust the parameter selected.

I need your advice to help me decide to go further.
Thank you very much.

-- 
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Re: [gmx-users] ligand moving out during umbrella sampling

2017-05-19 Thread abhisek Mondal

On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:

>
>
> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>
>> This time I think I got ligand restrained successfully during the umbrella
>> sampling. I have removed the restrain from protein, as per your advice.
>> Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
>> pull_rate1=0.0.
>> I have uploaded the trajectory movie (and other mdp files) in the
>> following
>> link:
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>
>> However, I'm facing a problem. Due to the withdrawal of the position
>> restrain of protein. The protein and ligand (together) is moving around
>> the
>> box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
>> than 0.49 times the box size (10.646989)" error.
>>
>> As per the video I have uploaded, if I assume this approach worked, then
>> how can I avoid this error ? Is  there any way to make sure the
>> protein-ligand remains in the middle of the box (or nearby). I have taken
>> pretty large box compared to the protein structure from the beginning.
>>
>> Please suggest me a way out.
>>
>>
> Use a larger box or use direction-periodic geometry.


 For the sake of computational power I'm leaning towards direction-periodic
geometry. However, from the mailing list entries I found out that pressure
coupling should not be used for this kind of geometry setup.
NVT coupling with no velocity generation is what I'm opting for. There are
a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
Would you please suggest if the code (
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0) looks
sensible ?

Eagerly waiting for your opinion.



>
> -Justin
>
>
> On Mon, May 15, 2017 at 5:48 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/15/17 2:45 AM, abhisek Mondal wrote:
>>>
>>> On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul  wrote:



> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>
> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal <
> abhisek.m...@gmail.com
>
>>
>>> wrote:
>>
>> Hi,
>>
>>
>>> Thank you for the explanation. It really cleared some concepts. But
>>> I'm
>>> still having my ligand moving in this step. I have modified the code
>>> as:
>>> ; Pull code
>>> pull= umbrella
>>> pull_ngroups= 1
>>> pull_group0 = Protein_chain_A
>>> pull_group1 = ACO
>>> pull_geometry   = direction ; simple distance increase
>>> pull_dim   = Y Y Y ; not to allow ligand move along
>>> other
>>> dir
>>> pull_rate1 = 0.0
>>> pull_k1   = 1000   ; kJ mol^-1 nm^-2
>>> pull_start   = yes   ; define initial COM distance > 0
>>> pull_vec1   = 0 0 -1
>>>
>>>
>>> Note that with "direction" geometry, only pull_vec1 is acting.
>>>
>> pull_dim
> is ignored.
>
> The ligand was previously moving along x,y direction when I was using
>
> pull_dim  = N N Y. So I changed it to Y in all direction and provided 0
>>
>>> as
>>> vector  and pull_rate1=0.0, so that it does not move much. But at the
>>> end
>>> of a 10ns run, I see that the ligand is still moving as it was
>>> earlier.
>>>
>>> It shows me:
>>>
>>>  Pull group  natoms  pbc atom  distance at start reference at t=0
>>0  1132936665
>>159  1618  -1.555-1.555
>> Is it ok withe negative value ? Anyway this setup is not working.
>>
>>
>> Again you're trying to just apply the restraint to one dimension and
>> it
>>
> looks to be fairly arbitrary.  I already suggested using the vector
> connecting the ligand COM with the binding site residues' COM and using
> that as pull_vec1.  Draw it out.  It makes a lot more sense than trying
> to
> restrain only along one axis, which as I have said before, makes no
> sense
> in this case.
>
> Thank you for such detailed suggestion.
>
> I followed on as per your suggestion. Calculated COM of protein and
 Ligand.
 Calculated protein-lig vector (using COM) to be used for pulling (as
 pull_vec1).
 Pulling also achieved successfully.
 But after pulling, when I performed the brief npt_umbrella run with
 pull_rate1=0, I found the ligand is moving little bit. Could not
 understand
 what I have mistaken this time.
 So I moved on for umbrella sampling mdrun step, with pull_rate1=0 and
 pull_vec1=as determined from COM calculations. Despite I found that the
 ligand is moving vigorously and got pulled away probably.
 I'm putting npt_umbrella.mdp,md_umbrella.mdp,conf140.gro(used for
 npt_umbrella), npt140.gro,md_umbrella run video in the following link:

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

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Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Re: [gmx-users] Error with moleculetype

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Re: [gmx-users] Need to confirm parameters.

[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

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Re: [gmx-users] ligand moving out during umbrella sampling

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

Re: [gmx-users] Need to confirm parameters.

[gmx-users] Need to confirm parameters.

Re: [gmx-users] ligand moving out during umbrella sampling

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