subject:"\[gmx\-users\] Grompp error"

Re: [gmx-users] grompp error : Atomtype CAro not found

2020-03-03 Thread Justin Lemkul





On 3/3/20 2:47 AM, Atila Petrosian wrote:

Dear Justin and Dallas,

Thanks for your answers. I am so confused. I am beginner in MD simulation
of lipid + small molecule.

'' There are far better options for lipids than the old Berger parameters
used in the tutorial. I wrote the tutorial in 2008 and it reflected a
common protocol at the time ''.
Justin, please suggest me better parameter for lipids, exactly (point out
the web site).


I suggest you spend some time investigating the literature as many 
comparison studies have been done. This is a critical choice that you 
must make in designing your simulation study. The force field you choose 
needs to adequately cover all the elements of your system, not just the 
lipids.



'' Since you are using ATB to generate the topology for your small
molecule, then it stands to reason that you then should use ATB for the
lipid molecule. '' Dallas, are you sure ATB can be used for lipids ???


Here I disagree with Dallas. Any robust force field already supports 
lipids and you should not have to rely on ATB to produce the lipid 
parameters, which will likely be less accurate than specifically 
parametrized entities.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] grompp error : Atomtype CAro not found

2020-03-02 Thread Atila Petrosian

Dear Justin and Dallas,

Thanks for your answers. I am so confused. I am beginner in MD simulation
of lipid + small molecule.

'' There are far better options for lipids than the old Berger parameters
used in the tutorial. I wrote the tutorial in 2008 and it reflected a
common protocol at the time ''.
Justin, please suggest me better parameter for lipids, exactly (point out
the web site).

'' Since you are using ATB to generate the topology for your small
molecule, then it stands to reason that you then should use ATB for the
lipid molecule. '' Dallas, are you sure ATB can be used for lipids ???

Best,
Atila
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Re: [gmx-users] grompp error : Atomtype CAro not found

2020-03-02 Thread Dallas Warren

You need to use the same forcefield.

Since you are using ATB to generate the topology for your small molecule,
then it stands to reason that you then should use ATB for the lipid
molecule.

Search ATB, I'm pretty sure the various lipids will already be there, and
suspect they will be some that the developers of the forcefield added
themselves, rather than a user submitting.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.

On Mon, 2 Mar 2020 at 18:40, Atila Petrosian 
wrote:

> Hi Dallas,
> thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB
> server.
>
> My system contains lipid molecules and small molecule. For lipid molecules,
> Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both
> of gromos54a7_atb.ff
> and  gromos53a6_lipid.ff in topology file.
>
> Please guide me.
>
> Best,
> Atila
> --
> Gromacs Users mailing list
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> * Please search the archive at
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Re: [gmx-users] grompp error : Atomtype CAro not found

2020-03-02 Thread Justin Lemkul





On 3/2/20 2:40 AM, Atila Petrosian wrote:

Hi Dallas,
thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB
server.

My system contains lipid molecules and small molecule. For lipid molecules,
Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both
of gromos54a7_atb.ff


I explicitly do not endorse/suggest the force field combination, as 
noted on the home page of that tutorial:


"*Please note*that the purpose of this tutorial is instructional, to 
build a membrane protein system and also to understand GROMACS force 
field organization and methods for modification. *This tutorial is not 
an endorsement or suggestion that you use these specific parameters for 
your simulation.* The approach taken here works well in the case where 
one needs to augment a parameter set with other parameters that have 
been derived in a consistent manner."


http://www.mdtutorials.com/gmx/membrane_protein/index.html

But in any event, the logic is the same if you need to augment any force 
field with new parameters (that are compatible with the parent force 
field). There are far better options for lipids than the old Berger 
parameters used in the tutorial. I wrote the tutorial in 2008 and it 
reflected a common protocol at the time. I have acknowledged within the 
tutorial that the force field and methods used are somewhat outdated but 
that the logic of extending a force field and using the tutorial as a 
vehicle to understand GROMACS force field organization remains valuable.


-Justin


and  gromos53a6_lipid.ff in topology file.

Please guide me.

Best,
Atila


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] grompp error : Atomtype CAro not found

2020-03-01 Thread Atila Petrosian

Hi Dallas,
thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB
server.

My system contains lipid molecules and small molecule. For lipid molecules,
Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both
of gromos54a7_atb.ff
and  gromos53a6_lipid.ff in topology file.

Please guide me.

Best,
Atila
-- 
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Re: [gmx-users] grompp error : Atomtype CAro not found

2020-03-01 Thread Dallas Warren

Did you read what the ATB told you about the topologies it generates, and
what forcefield you have to use?  There is a warning posted on the page
where you download your topology files that applies directly to this error
you have encountered:

"*Warning!* This molecule contains non-standard atom types not included in
the standard GROMOS 54A7 forcefield. To use these atom types the internal
GROMACS parameter files must be updated. These can be downloaded using the
link below. Instructions on where to place (and how to use) the files are
provided in the README file included in the archive."

ATB uses GROMOS 54a7 ATB, and you have to download and use that forcefield
for any molecules you generate using that server.  You cannot just mix it
with GROMOS 53a6 like you have tried to, since 54a7_atb has additional atom
types.

Stick with a single forcefield, do not mix then because the vast majority
are not compatible in that manner.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.

On Sun, 1 Mar 2020 at 19:41, Atila Petrosian 
wrote:

> Hi gromacs users,
>
> I am doing MD simulation of my system (DPPC lipid + 2 drug molecules +
> water molecules) using gromacs 2019.
>
> I used ATB for drug molecules and Membrane Protein: KALP15 in DPPC
> gromacs tutorial method for lipid molecules (based on Justin Lemkul
> suggestion in my previous post:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2020-February/128420.html
> ).
>
> ---
> My topology file is as follows:
> ---
> ; Include forcefield parameters
> #include "gromos53a6_lipid.ff/forcefield.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include DPPC chain topology
> #include "dppc.itp"
>
> ; Include drug topology
> #include "lig.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>
> [ system ]
> ; Name
> dopc/lig/sol in water
>
> [ molecules ]
> ; Compound#mols
> DPPC   128
> LIG  2
> SOL   8257
> ---
> My lig.itp file is as follows:
> ---
> .
> .
> ;
> [ moleculetype ]
> ; Name   nrexcl
> LIG 3
>
> [ atoms ]
> ;  nr  type  resnr  resid  atom  cgnr  chargemass
> 1HC1LIGH2710.131   1.0080
> 2  CAro1LIGC242   -0.130  12.0110
> 3  CAro1LIGC233   -0.130  12.0110
> 4HC1LIGH2640.131   1.0080
> 5  CAro1LIGC225   -0.119  12.0110
> 6HC1LIGH2560.135   1.0080
> 7  CAro1LIGC217   -0.039  12.0110
> 8  CAro1LIGC268   -0.119  12.0110
> 9HC1LIGH2990.135   1.0080
>10  CAro1LIGC25   10   -0.130  12.0110
>11HC1LIGH28   110.131   1.0080
>12 C1LIGC18   12   -0.051  12.0110
>13   CH21LIGC19   130.055  14.0270
>14   CH31LIGC20   140.020  15.0350
>15  CAro1LIGC11   15   -0.025  12.0110
>16  CAro1LIGC12   16   -0.040  12.0110
>17  CAro1LIGC13   17   -0.117  12.0110
>18HC1LIGH15   180.137   1.0080
>19  CAro1LIGC14   19   -0.133  12.0110
>20HC1LIGH16   200.131   1.0080
>21  CAro1LIGC15   21   -0.129  12.0110
>22HC1LIGH17   220.131   1.0080
>23  CAro1LIGC16   23   -0.133  12.0110
>24HC1LIGH18   240.131   1.0080
>25  CAro1LIGC17   25   -0.117  12.0110
>26HC1LIGH19   260.137   1.0080
>27  CAro1LIG C8   27   -0.076  12.0110
>28  CAro1LIG C7   28   -0.079  12.0110
>29HC1LIGH12   290.139   1.0080
>30  CAro1LIG C6   30   -0.184  12.0110
>31HC1LIGH11   310.143   1.0080
>32  CAro1LIG C5   320.087  12.0110
>33  CAro1LIGC10   33   -0.184  12.0110
>34HC1LIGH14   340.143   1.0080
>35  CAro1LIG C9   35   -0.079  12.0110
>36HC1LIGH13   360.139   1.0080
>37OE1LIG O1   37   -0.219  15.9994
>38   CH21LIG C4   380.149  14.0270
>39   CH21LIG C3   390.101  14.0270
>40  NTer1LIG N1   40   -0.267  14.0067

[gmx-users] grompp error : Atomtype CAro not found

2020-03-01 Thread Atila Petrosian

Hi gromacs users,

I am doing MD simulation of my system (DPPC lipid + 2 drug molecules +
water molecules) using gromacs 2019.

I used ATB for drug molecules and Membrane Protein: KALP15 in DPPC
gromacs tutorial method for lipid molecules (based on Justin Lemkul
suggestion in my previous post:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2020-February/128420.html
).

---
My topology file is as follows:
---
; Include forcefield parameters
#include "gromos53a6_lipid.ff/forcefield.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include DPPC chain topology
#include "dppc.itp"

; Include drug topology
#include "lig.itp"

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

[ system ]
; Name
dopc/lig/sol in water

[ molecules ]
; Compound#mols
DPPC   128
LIG  2
SOL   8257
---
My lig.itp file is as follows:
---
.
.
;
[ moleculetype ]
; Name   nrexcl
LIG 3

[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemass
1HC1LIGH2710.131   1.0080
2  CAro1LIGC242   -0.130  12.0110
3  CAro1LIGC233   -0.130  12.0110
4HC1LIGH2640.131   1.0080
5  CAro1LIGC225   -0.119  12.0110
6HC1LIGH2560.135   1.0080
7  CAro1LIGC217   -0.039  12.0110
8  CAro1LIGC268   -0.119  12.0110
9HC1LIGH2990.135   1.0080
   10  CAro1LIGC25   10   -0.130  12.0110
   11HC1LIGH28   110.131   1.0080
   12 C1LIGC18   12   -0.051  12.0110
   13   CH21LIGC19   130.055  14.0270
   14   CH31LIGC20   140.020  15.0350
   15  CAro1LIGC11   15   -0.025  12.0110
   16  CAro1LIGC12   16   -0.040  12.0110
   17  CAro1LIGC13   17   -0.117  12.0110
   18HC1LIGH15   180.137   1.0080
   19  CAro1LIGC14   19   -0.133  12.0110
   20HC1LIGH16   200.131   1.0080
   21  CAro1LIGC15   21   -0.129  12.0110
   22HC1LIGH17   220.131   1.0080
   23  CAro1LIGC16   23   -0.133  12.0110
   24HC1LIGH18   240.131   1.0080
   25  CAro1LIGC17   25   -0.117  12.0110
   26HC1LIGH19   260.137   1.0080
   27  CAro1LIG C8   27   -0.076  12.0110
   28  CAro1LIG C7   28   -0.079  12.0110
   29HC1LIGH12   290.139   1.0080
   30  CAro1LIG C6   30   -0.184  12.0110
   31HC1LIGH11   310.143   1.0080
   32  CAro1LIG C5   320.087  12.0110
   33  CAro1LIGC10   33   -0.184  12.0110
   34HC1LIGH14   340.143   1.0080
   35  CAro1LIG C9   35   -0.079  12.0110
   36HC1LIGH13   360.139   1.0080
   37OE1LIG O1   37   -0.219  15.9994
   38   CH21LIG C4   380.149  14.0270
   39   CH21LIG C3   390.101  14.0270
   40  NTer1LIG N1   40   -0.267  14.0067
   41   CH31LIG C1   410.097  15.0350
   42   CH31LIG C2   420.097  15.0350
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0 c1
122   0.1090   1.2300e+07
232   0.1390   8.6600e+06
.
.
.
---
After using command: gmx grompp -f em1.mdp -c system.gro -p topol.top -o
em1.tpr,
I encountered with the following error:
---
ERROR 1 [file lig.itp, line 66]:
  Atomtype CAro not found
---
How to resole it?

Best,
Atila
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Re: [gmx-users] grompp error : Atomtype HC not found

2020-02-14 Thread Justin Lemkul





On 2/14/20 6:09 AM, Atila Petrosian wrote:

Dear Justin,
Thanks for answer.

You said " There is no reason to use this totally obsolete force field
(ffgmx.itp)".
I used ffgmx.itp, because there was a example.top file in Tieleman's web
site:


That example is almost as old as I am :) It reproduces published work 
but no longer reflects the state of the art. ffgmx (the "GROMACS force 
field," which is a terrible name for a hacked/partially undocumented 
GROMOS87) is no longer acceptable for modern simulations. Please see a 
more updated approach that uses GROMOS96 at 
http://www.mdtutorials.com/gmx/membrane_protein/index.html though I will 
note that the Berger parameters that are distributed by Tieleman and 
used in that tutorial are also not as high-quality as other more modern 
parameter sets like Slipids and CHARMM36.


-Justin


---
; topology for 1 alm molecule, 128 popc lipids, water and 1 counter ion
; alm.itp can be made in a straightforward manner with pdb2gmx, starting
; with a pdb file of alamethicin.
; make sure lipid.itp, popc.itp and alm.itp are in a location where
; grompp can find them (GMXLIB, current directory, or directory given in
; the .mdp file with the include option.
#include "ffgmx.itp"
#include "lipid.itp"
#include "popc.itp"
#include "alm.itp"
#include "ions.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
Alm on surf + relaxed popc

[ molecules ]
; name number
Protein 1
POPC128
SOL 3552
Na  1
---
Based on your suggestion, I used following in my topology file (I deleted
ffgmx.itp):

#include "lipid.itp"
#include "dppc.itp"
#include "lig.itp"
---
But I encountered with:
---
Fatal error:
Syntax error - File lipid.itp, line 11
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
---
lipid.itp file from Tieleman's web site is as follows:
---
;; this forcefield is a mixture of lipid and GROMOS parameters. GROMOS
;; parameters taken from ffgmxnb.itp, lipid parameters from Berger et
;; al, Biophys. J. 72, pp. 2002-2013. Parameters starting with L are
;; lipid parameter. LP2 and LP3 are Bergers pentadecane parameters,
;; the rest is OPLS. The lipids see SPC/SPCE, and lipids as
;; OPLS/Berger, protein as GROMOS, the protein sees lipids as GROMOS.

[ defaults ]
1   1

[ atomtypes ]
;name mass charge ptype  c6   c12
;
LO15.99940.000  A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS
   LOM15.99940.000  A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS
   LNL14.00670.000  A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS
LC12.01100.000  A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS
   LH113.01900.000  A 4.03100e-03 1.21400e-05 ;CH1, OPLS
   LH214.02700.000  A 7.00200e-03 2.48300e-05 ;CH2, OPLS
LP30.97380.000  A 9.16000e-03 2.50700e-05 ;phosphor, OPLS
   LOS15.99940.000  A 2.56300e-03 1.86800e-06 ;ester oxygen, OPLS
   LP214.02700.000  A 5.87400e-03 2.26500e-05 ;RB CH2, Bergers LJ
   LP315.03500.000  A 8.77700e-03 3.38500e-05 ;RB CH3, Bergers LJ
   LC315.03500.000  A 9.35700e-03 3.60900e-05 ;CH3, OPLS
   LC214.02700.000  A 5.94700e-03 1.79000e-05 ;CH2, OPLS
   ---

How to resolve that?

Best,
Atila


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

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[gmx-users] grompp error : Atomtype HC not found

2020-02-14 Thread Atila Petrosian

Dear Justin,
Thanks for answer.

You said " There is no reason to use this totally obsolete force field
(ffgmx.itp)".
I used ffgmx.itp, because there was a example.top file in Tieleman's web
site:
---
; topology for 1 alm molecule, 128 popc lipids, water and 1 counter ion
; alm.itp can be made in a straightforward manner with pdb2gmx, starting
; with a pdb file of alamethicin.
; make sure lipid.itp, popc.itp and alm.itp are in a location where
; grompp can find them (GMXLIB, current directory, or directory given in
; the .mdp file with the include option.
#include "ffgmx.itp"
#include "lipid.itp"
#include "popc.itp"
#include "alm.itp"
#include "ions.itp"

#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

[ system ]
; name
Alm on surf + relaxed popc

[ molecules ]
; name number
Protein 1
POPC128
SOL 3552
Na  1
---
Based on your suggestion, I used following in my topology file (I deleted
ffgmx.itp):

#include "lipid.itp"
#include "dppc.itp"
#include "lig.itp"
---
But I encountered with:
---
Fatal error:
Syntax error - File lipid.itp, line 11
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
---
lipid.itp file from Tieleman's web site is as follows:
---
;; this forcefield is a mixture of lipid and GROMOS parameters. GROMOS
;; parameters taken from ffgmxnb.itp, lipid parameters from Berger et
;; al, Biophys. J. 72, pp. 2002-2013. Parameters starting with L are
;; lipid parameter. LP2 and LP3 are Bergers pentadecane parameters,
;; the rest is OPLS. The lipids see SPC/SPCE, and lipids as
;; OPLS/Berger, protein as GROMOS, the protein sees lipids as GROMOS.

[ defaults ]
1   1

[ atomtypes ]
;name mass charge ptype  c6   c12
;
   LO15.99940.000  A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS
  LOM15.99940.000  A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS
  LNL14.00670.000  A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS
   LC12.01100.000  A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS
  LH113.01900.000  A 4.03100e-03 1.21400e-05 ;CH1, OPLS
  LH214.02700.000  A 7.00200e-03 2.48300e-05 ;CH2, OPLS
   LP30.97380.000  A 9.16000e-03 2.50700e-05 ;phosphor, OPLS
  LOS15.99940.000  A 2.56300e-03 1.86800e-06 ;ester oxygen, OPLS
  LP214.02700.000  A 5.87400e-03 2.26500e-05 ;RB CH2, Bergers LJ
  LP315.03500.000  A 8.77700e-03 3.38500e-05 ;RB CH3, Bergers LJ
  LC315.03500.000  A 9.35700e-03 3.60900e-05 ;CH3, OPLS
  LC214.02700.000  A 5.94700e-03 1.79000e-05 ;CH2, OPLS
  ---

How to resolve that?

Best,
Atila
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Re: [gmx-users] grompp error : Atomtype HC not found

2020-02-13 Thread Justin Lemkul





On 2/13/20 8:56 AM, Atila Petrosian wrote:

Hi gromacs users,

I am doing MD simulation of my system (DPPC lipid + 2 drug molecules +
water molecules) using gromacs 2019.

I used ATB for drug molecules and Tieleman's web site for lipid molecules.


ATB uses a custom version of GROMOS96 that uses new atom types. You need 
to use their force field files.



---
My topology file is as follows:
---
#include "ffgmx.itp"


There is no reason to use this totally obsolete force field.

-Justin


#include "lipid.itp"
#include "dppc.itp"
#include "lig.itp"

#ifdef POSRES_LIG
#include "lig_posre.itp"
#endif

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

[ system ]
; name
dppc/lig/lig/sol

[ molecules ]
; Compound#mols
DPP128
LIG  2
SOL   7173
---
My lig.itp file is as follows:
---
.
.
.
.
;
[ moleculetype ]
; Name   nrexcl
LIG 3

[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemass
 1HC1LIGH2710.131   1.0080
 2  CAro1LIGC242   -0.130  12.0110
 3  CAro1LIGC233   -0.130  12.0110
 4HC1LIGH2640.131   1.0080
 5  CAro1LIGC225   -0.119  12.0110
 6HC1LIGH2560.135   1.0080
 7  CAro1LIGC217   -0.039  12.0110
 8  CAro1LIGC268   -0.119  12.0110
 9HC1LIGH2990.135   1.0080
10  CAro1LIGC25   10   -0.130  12.0110
11HC1LIGH28   110.131   1.0080
12 C1LIGC18   12   -0.051  12.0110
13   CH21LIGC19   130.055  14.0270
14   CH31LIGC20   140.020  15.0350
15  CAro1LIGC11   15   -0.025  12.0110
16  CAro1LIGC12   16   -0.040  12.0110
17  CAro1LIGC13   17   -0.117  12.0110
18HC1LIGH15   180.137   1.0080
19  CAro1LIGC14   19   -0.133  12.0110
20HC1LIGH16   200.131   1.0080
21  CAro1LIGC15   21   -0.129  12.0110
22HC1LIGH17   220.131   1.0080
23  CAro1LIGC16   23   -0.133  12.0110
24HC1LIGH18   240.131   1.0080
25  CAro1LIGC17   25   -0.117  12.0110
26HC1LIGH19   260.137   1.0080
27  CAro1LIG C8   27   -0.076  12.0110
28  CAro1LIG C7   28   -0.079  12.0110
29HC1LIGH12   290.139   1.0080
30  CAro1LIG C6   30   -0.184  12.0110
31HC1LIGH11   310.143   1.0080
32  CAro1LIG C5   320.087  12.0110
33  CAro1LIGC10   33   -0.184  12.0110
34HC1LIGH14   340.143   1.0080
35  CAro1LIG C9   35   -0.079  12.0110
36HC1LIGH13   360.139   1.0080
37OE1LIG O1   37   -0.219  15.9994
38   CH21LIG C4   380.149  14.0270
39   CH21LIG C3   390.101  14.0270
40  NTer1LIG N1   40   -0.267  14.0067
41   CH31LIG C1   410.097  15.0350
42   CH31LIG C2   420.097  15.0350
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0 c1
 122   0.1090   1.2300e+07
 232   0.1390   8.6600e+06
.
.
.
.
.
---
After using command: gmx solvate -cp final.gro -cs spc216.gro -p topol.top
-o system.gro, I encountered with the following error:
---
ERROR 1 [file lig.itp, line 65]:
   Atomtype HC not found
   ---

How to resole it?

Best,
Atila


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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[gmx-users] grompp error : Atomtype HC not found

2020-02-13 Thread Atila Petrosian

Hi gromacs users,

I am doing MD simulation of my system (DPPC lipid + 2 drug molecules +
water molecules) using gromacs 2019.

I used ATB for drug molecules and Tieleman's web site for lipid molecules.
---
My topology file is as follows:
---
#include "ffgmx.itp"
#include "lipid.itp"
#include "dppc.itp"
#include "lig.itp"

#ifdef POSRES_LIG
#include "lig_posre.itp"
#endif

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

[ system ]
; name
dppc/lig/lig/sol

[ molecules ]
; Compound#mols
DPP128
LIG  2
SOL   7173
---
My lig.itp file is as follows:
---
.
.
.
.
;
[ moleculetype ]
; Name   nrexcl
LIG 3

[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemass
1HC1LIGH2710.131   1.0080
2  CAro1LIGC242   -0.130  12.0110
3  CAro1LIGC233   -0.130  12.0110
4HC1LIGH2640.131   1.0080
5  CAro1LIGC225   -0.119  12.0110
6HC1LIGH2560.135   1.0080
7  CAro1LIGC217   -0.039  12.0110
8  CAro1LIGC268   -0.119  12.0110
9HC1LIGH2990.135   1.0080
   10  CAro1LIGC25   10   -0.130  12.0110
   11HC1LIGH28   110.131   1.0080
   12 C1LIGC18   12   -0.051  12.0110
   13   CH21LIGC19   130.055  14.0270
   14   CH31LIGC20   140.020  15.0350
   15  CAro1LIGC11   15   -0.025  12.0110
   16  CAro1LIGC12   16   -0.040  12.0110
   17  CAro1LIGC13   17   -0.117  12.0110
   18HC1LIGH15   180.137   1.0080
   19  CAro1LIGC14   19   -0.133  12.0110
   20HC1LIGH16   200.131   1.0080
   21  CAro1LIGC15   21   -0.129  12.0110
   22HC1LIGH17   220.131   1.0080
   23  CAro1LIGC16   23   -0.133  12.0110
   24HC1LIGH18   240.131   1.0080
   25  CAro1LIGC17   25   -0.117  12.0110
   26HC1LIGH19   260.137   1.0080
   27  CAro1LIG C8   27   -0.076  12.0110
   28  CAro1LIG C7   28   -0.079  12.0110
   29HC1LIGH12   290.139   1.0080
   30  CAro1LIG C6   30   -0.184  12.0110
   31HC1LIGH11   310.143   1.0080
   32  CAro1LIG C5   320.087  12.0110
   33  CAro1LIGC10   33   -0.184  12.0110
   34HC1LIGH14   340.143   1.0080
   35  CAro1LIG C9   35   -0.079  12.0110
   36HC1LIGH13   360.139   1.0080
   37OE1LIG O1   37   -0.219  15.9994
   38   CH21LIG C4   380.149  14.0270
   39   CH21LIG C3   390.101  14.0270
   40  NTer1LIG N1   40   -0.267  14.0067
   41   CH31LIG C1   410.097  15.0350
   42   CH31LIG C2   420.097  15.0350
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0 c1
122   0.1090   1.2300e+07
232   0.1390   8.6600e+06
.
.
.
.
.
---
After using command: gmx solvate -cp final.gro -cs spc216.gro -p topol.top
-o system.gro, I encountered with the following error:
---
ERROR 1 [file lig.itp, line 65]:
  Atomtype HC not found
  ---

How to resole it?

Best,
Atila
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Re: [gmx-users] grompp error: Unknown bond_atomtype

2019-04-09 Thread Justin Lemkul




On 4/1/19 5:28 AM, vico...@fizyka.umk.pl wrote:

Dear Professor Lemkul,

You have written that I mix amber and charmm  forcefields. It is kinda 
intiguing, becuase I downloaded lipid parameteres in amber and the 
atom names in the files are exactly the same as charmm-gui pdb output.




Atom *names* in a coordinate file are an entirely different concept from 
atom *types* in a force field parameter set.


I attach membrane pdb and parameter file. I would be very thankfull if 
you would take a look and judge if these are consistent. As I said - 
pdb2gmx worked well with these files, only grompp got troubles with 
"Unknown bond_atomtype CTL3". If CTL3 atom  is characteristic for 
charmm ff why these names are used in amber files?




I don't have nearly enough information to help you answer that question. 
But you've got an unknown atom type in your topology, that much is clear.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] grompp error: Unknown bond_atomtype

2019-03-26 Thread Justin Lemkul




On 3/26/19 8:22 AM, vico...@fizyka.umk.pl wrote:

Hello everyone,

I would call myself newbie gromacs user and need some help with task 
that was given to me. I'm supposed to take protein-ligand complex 
(bounded by covalence bond) and put it  into membrane. I'm glad I've 
created the complex in amber force field. But now I stucked around 
membrane think.


I have created DLPC-only membrane cluster in charmm-gui. I have found 
parameters for this type of lipid. I did add additional names for atom 
 in  atomtypes.atp, include ffbonded_lipid.itp and 
ffnonbonded_lipit.itp files to forcefrield.itp and put into amber 
forcefield directory t he lipids.rtp file. Gladly  everything went 
smoothly with pdb2gmx  with my membrane. I get topol.top file. Then I 
wanted to try minimize energy. I've prepared .mdp file and used gromp 
with:


gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr

Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is 
defined in atomtypes.atp  and the bond have its parameters inside the 
ffbond.itp file. It's really strange for me, beacuse I thought that if 
topol.top file was created there is no possibility to get some 
troubles with defined atoms, bonds, etc.


Where did I make mistake?


It looks like you're mixing force fields between AMBER and CHARMM. CTL3 
is a CHARMM atom type. You cannot mix force fields; you must develop the 
topology under a single, consistent parameter set.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] grompp error: Unknown bond_atomtype

2019-03-26 Thread vicolls

Cytowanie RAHUL SURESH :

On Tue 26 Mar, 2019, 6:18 PM ,  wrote:

Cytowanie RAHUL SURESH :

> On Tue 26 Mar, 2019, 6:00 PM ,  wrote:
>
>> Hello everyone,
>>
>> I would call myself newbie gromacs user and need some help with task
>> that was given to me. I'm supposed to take protein-ligand complex
>> (bounded by covalence bond) and put it  into membrane. I'm glad I've
>> created the complex in amber force field. But now I stucked around
>> membrane think.
>>
>> I have created DLPC-only membrane cluster in charmm-gui. I have found
>> parameters for this type of lipid. I did add additional names for atom
>>   in  atomtypes.atp, include ffbonded_lipid.itp and
>> ffnonbonded_lipit.itp files to forcefrield.itp and put into amber
>> forcefield directory t he lipids.rtp file. Gladly  everything went
>> smoothly with pdb2gmx  with my membrane. I get topol.top file. Then I
>> wanted to try minimize energy. I've prepared .mdp file and used gromp
>> with:
>>
>> gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr
>>
>> Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is
>> defined in atomtypes.atp  and the bond have its parameters inside the
>> ffbond.itp file. It's really strange for me, beacuse I thought that if
>> topol.top file was created there is no possibility to get some
>> troubles with defined atoms, bonds, etc.
>>
> This CTL3 is that of ligand?

No, I'm  doing right now ONLY membrane. There are only lipids in the
.gro file with solvataion and the CTL3 is atom of lipid. I just wanted
to check if I'm able to create membrane-only system first.  If
everything will work I'll  try  to embed protein+ligand in  this
membrane.

If I believe you are using amber ff for the lipids generated using charm
GUI, then I should say the nomenclature of the lipid membrane will be in
charmm format. Either you must use charmm ff or you have to use lipids for
amber ff ..

I just download PDB file with membrane cluster structure from  
charmm-gui. No topology, no parameters at all. Only coordinates. Then  
I found parameters in amber force field for this DLPC and proceeded  
both pdb structure and parameters .itp with pdb2gmx. Everything  
worked.  But now got troubles with energy minimization/simulations.

>>
>
>>
>
>
>> --
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Re: [gmx-users] grompp error: Unknown bond_atomtype

2019-03-26 Thread RAHUL SURESH

On Tue 26 Mar, 2019, 6:18 PM ,  wrote:

> Cytowanie RAHUL SURESH :
>
> > On Tue 26 Mar, 2019, 6:00 PM ,  wrote:
> >
> >> Hello everyone,
> >>
> >> I would call myself newbie gromacs user and need some help with task
> >> that was given to me. I'm supposed to take protein-ligand complex
> >> (bounded by covalence bond) and put it  into membrane. I'm glad I've
> >> created the complex in amber force field. But now I stucked around
> >> membrane think.
> >>
> >> I have created DLPC-only membrane cluster in charmm-gui. I have found
> >> parameters for this type of lipid. I did add additional names for atom
> >>   in  atomtypes.atp, include ffbonded_lipid.itp and
> >> ffnonbonded_lipit.itp files to forcefrield.itp and put into amber
> >> forcefield directory t he lipids.rtp file. Gladly  everything went
> >> smoothly with pdb2gmx  with my membrane. I get topol.top file. Then I
> >> wanted to try minimize energy. I've prepared .mdp file and used gromp
> >> with:
> >>
> >> gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr
> >>
> >> Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is
> >> defined in atomtypes.atp  and the bond have its parameters inside the
> >> ffbond.itp file. It's really strange for me, beacuse I thought that if
> >> topol.top file was created there is no possibility to get some
> >> troubles with defined atoms, bonds, etc.
> >>
> > This CTL3 is that of ligand?
>
> No, I'm  doing right now ONLY membrane. There are only lipids in the
> .gro file with solvataion and the CTL3 is atom of lipid. I just wanted
> to check if I'm able to create membrane-only system first.  If
> everything will work I'll  try  to embed protein+ligand in  this
> membrane.
>
> If I believe you are using amber ff for the lipids generated using charm
> GUI, then I should say the nomenclature of the lipid membrane will be in
> charmm format. Either you must use charmm ff or you have to use lipids for
> amber ff ..
> >>
> >
> > Where did I make mistake?
> >>
> >> Have did you manage to add ligand topology?
> >>
> >
> >
> >> --
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> >> posting!
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> >>
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>
>
>
>
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Re: [gmx-users] grompp error: Unknown bond_atomtype

2019-03-26 Thread vicolls


Cytowanie RAHUL SURESH :


On Tue 26 Mar, 2019, 6:00 PM ,  wrote:


Hello everyone,

I would call myself newbie gromacs user and need some help with task
that was given to me. I'm supposed to take protein-ligand complex
(bounded by covalence bond) and put it  into membrane. I'm glad I've
created the complex in amber force field. But now I stucked around
membrane think.

I have created DLPC-only membrane cluster in charmm-gui. I have found
parameters for this type of lipid. I did add additional names for atom
  in  atomtypes.atp, include ffbonded_lipid.itp and
ffnonbonded_lipit.itp files to forcefrield.itp and put into amber
forcefield directory t he lipids.rtp file. Gladly  everything went
smoothly with pdb2gmx  with my membrane. I get topol.top file. Then I
wanted to try minimize energy. I've prepared .mdp file and used gromp
with:

gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr

Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is
defined in atomtypes.atp  and the bond have its parameters inside the
ffbond.itp file. It's really strange for me, beacuse I thought that if
topol.top file was created there is no possibility to get some
troubles with defined atoms, bonds, etc.


This CTL3 is that of ligand?


No, I'm  doing right now ONLY membrane. There are only lipids in the  
.gro file with solvataion and the CTL3 is atom of lipid. I just wanted  
to check if I'm able to create membrane-only system first.  If  
everything will work I'll  try  to embed protein+ligand in  this  
membrane.






Where did I make mistake?


Have did you manage to add ligand topology?





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Re: [gmx-users] grompp error: Unknown bond_atomtype

2019-03-26 Thread RAHUL SURESH

On Tue 26 Mar, 2019, 6:00 PM ,  wrote:

> Hello everyone,
>
> I would call myself newbie gromacs user and need some help with task
> that was given to me. I'm supposed to take protein-ligand complex
> (bounded by covalence bond) and put it  into membrane. I'm glad I've
> created the complex in amber force field. But now I stucked around
> membrane think.
>
> I have created DLPC-only membrane cluster in charmm-gui. I have found
> parameters for this type of lipid. I did add additional names for atom
>   in  atomtypes.atp, include ffbonded_lipid.itp and
> ffnonbonded_lipit.itp files to forcefrield.itp and put into amber
> forcefield directory t he lipids.rtp file. Gladly  everything went
> smoothly with pdb2gmx  with my membrane. I get topol.top file. Then I
> wanted to try minimize energy. I've prepared .mdp file and used gromp
> with:
>
> gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr
>
> Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is
> defined in atomtypes.atp  and the bond have its parameters inside the
> ffbond.itp file. It's really strange for me, beacuse I thought that if
> topol.top file was created there is no possibility to get some
> troubles with defined atoms, bonds, etc.
>
> This CTL3 is that of ligand?
>

Where did I make mistake?
>
> Have did you manage to add ligand topology?
>


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[gmx-users] grompp error: Unknown bond_atomtype

2019-03-26 Thread vicolls


Hello everyone,

I would call myself newbie gromacs user and need some help with task  
that was given to me. I'm supposed to take protein-ligand complex  
(bounded by covalence bond) and put it  into membrane. I'm glad I've  
created the complex in amber force field. But now I stucked around  
membrane think.


I have created DLPC-only membrane cluster in charmm-gui. I have found  
parameters for this type of lipid. I did add additional names for atom  
 in  atomtypes.atp, include ffbonded_lipid.itp and  
ffnonbonded_lipit.itp files to forcefrield.itp and put into amber  
forcefield directory t he lipids.rtp file. Gladly  everything went  
smoothly with pdb2gmx  with my membrane. I get topol.top file. Then I  
wanted to try minimize energy. I've prepared .mdp file and used gromp  
with:


gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr

Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is  
defined in atomtypes.atp  and the bond have its parameters inside the  
ffbond.itp file. It's really strange for me, beacuse I thought that if  
topol.top file was created there is no possibility to get some  
troubles with defined atoms, bonds, etc.


Where did I make mistake?


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[gmx-users] Grompp error

2019-03-24 Thread Hanin Omar

Hello everyone
I am using gromacs version 2019, and I want to add dihedral restraint to the 
backbone of the last helix in my protein in my simulation, however grompp gives 
me this error
ERROR 1 [file D2-TorisionRes.itp, line 5]:
  Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest.
  (after the function type).

from my understanding this means that i am missing one feild in my restraint 
file, can someone tell me what is it?This is the content of my 
D2-TorisionRes.itp file :[ dihedral_restraints ]
;For the second domain starting from residue 74
; ai    aj ak  al   type   label   phi   dphi   kfac   power
;  C(i-1)   Ni  C-alphai   Ci 1    1   value   0  1.0    2.0  
   1159    1174  1175 1176    1    1  -70.2    0  1.0    2.0  ;res 
74
   1176    1186  1187 1188    1    1  -91.0    0  1.0    2.0  ;res 
75
   1188    1205  1206 1207    1    1  -53.4    0  1.0    2.0  ;res 
76

and in my topology file i added this line after the molecule:; Include Dihedral 
restraint file
#ifdef DIHRE
#include "D2-TorisionRes.itp"
#endif

and in my mdp file i used:define   = -DDIHRE


is my implementation of the dihedral restraint correct so far? also do i have 
to include them in all the equiliberation steps?
THank you for the help

Sent from my iPhone
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Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-20 Thread Mark Abraham

Hi,

The large energy means your topology is probably broken. Please use a tool
that will write an .itp file for you (e.g. SwissParam?), or next time get
your topology for your ligand working before you try to use it in a
complex. Even get a simple form of the ligand working first, to teach
yourself the process of writing the coordinate file. The more new things
you try to do at once, the less likely you are to fail in ways that you can
help yourself to fix.

Mark

On Wed, Dec 20, 2017 at 8:24 PM RAHUL SURESH 
wrote:

> To be included here, the ligand I have uploaded seems to be so congested
> and out of form. Look literally like a clumsy ball.
> I am not sure what make this happen.
>
> On Wed, Dec 20, 2017 at 2:51 PM, RAHUL SURESH 
> wrote:
>
> > Dear Alex
> >
> > I have tried that but the system collapse. For em_real.mdp option,I get
> > message stating
> >
> > Energy minimization has stopped, but the forces have not converged to the
> > requested precision Fmax < 1000 (which may not be possible for your
> > system).
> > It stopped because the algorithm tried to make a new step whose size was
> > too
> > small, or there was no change in the energy since last step. Either way,
> we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, but this is often
> not
> > needed for preparing to run molecular dynamics.
> > You might need to increase your constraint accuracy, or turn
> > off constraints altogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Back Off! I just backed up em.gro to ./#em.gro.1#
> >
> > Steepest Descents converged to machine precision in 15 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy  =  3.9192084e+11
> > Maximum force =  1.3457252e+14 on atom 629
> > Norm of force =  1.0629695e+12
> >
> > Simulation ended prematurely, no performance report will be written.
> >
> > GROMACS reminds you: "When It Starts to Start It'll Never Stop"
> (Magnapop)
> >
> >
> > On Wed, Dec 20, 2017 at 2:20 PM, Alex  wrote:
> >
> >> The description for the Urey-Bradley potential (assuming two quadratic
> >> terms qualify for the proud term "potential") is described in the user
> >> manual, and the constants' order of appearance in the itp file is given
> in
> >> the Table 5.5 of the manual. If you have a basic quadratic angular term
> >> (first term in U-B with two constants) from elsewhere and you want to
> use
> >> it in the U-B format, it is an absolutely trivial task. All you have to
> do
> >> is set the U-B distance-dependent energy component to zero.
> >>
> >> Alex
> >>
> >>
> >>
> >> On 12/20/2017 12:05 AM, RAHUL SURESH wrote:
> >>
> >>> Hi
> >>>
> >>> Thank you Mark.
> >>>
> >>> On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> >>> >
> >>> wrote:
> >>>
> >>> Hi,
> 
>  Sorry I don't know how any of these non-GROMACS tools work, or even
>  whether
>  they actually generate Urey Bradley interactions that have all the
>  terms. I
>  suggest you spend some time with the documentation.
> 
>  Mark
> 
>  On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH 
>  wrote:
> 
>  Sorry Mark, I failed to note that.
> >
> > I am afraid that I don't know what that are those components and how
> > and
> > where to find it. If you are actually meaning about "ub0 kub"
> >
>  components,
> 
> > how could i find the value for it. In case of swiss param generated
> itp
> > file, these components appear to be 0. Any help here please?
> >
> >
> > On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham <
> > mark.j.abra...@gmail.com
> >
> > wrote:
> >
> > Hi,
> >>
> >> Please read my answer.
> >>
> >> Mark
> >>
> >> On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH  >
> >> wrote:
> >>
> >> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul 
> >>>
> >> wrote:
> 
> >
>  On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> 
> > Dear all
> >
> > For grompp em.mdp I get an error
> >
> > ERROR 1 [file THC.itp, line 89]:
> > Incorrect number of parameters - found 2, expected 4 or 8 for
> >
>  U-B.
> >
> >> My itp file as follows
> >
> > [ angles ]
> >
> > 1   2   29   579.178   109.588 *{Line 89}*
> > 1   2   3 532.192   112.817
> > 2   3   31   551.424   109.189
> >
> >   From the manual chapter 5, function of U-B is 5. And it works
> >
>  fine
> 
> > for
> >>
> >>> function type 2 and 8.
> >
> >

Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-20 Thread RAHUL SURESH

To be included here, the ligand I have uploaded seems to be so congested
and out of form. Look literally like a clumsy ball.
I am not sure what make this happen.

On Wed, Dec 20, 2017 at 2:51 PM, RAHUL SURESH 
wrote:

> Dear Alex
>
> I have tried that but the system collapse. For em_real.mdp option,I get
> message stating
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up em.gro to ./#em.gro.1#
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  3.9192084e+11
> Maximum force =  1.3457252e+14 on atom 629
> Norm of force =  1.0629695e+12
>
> Simulation ended prematurely, no performance report will be written.
>
> GROMACS reminds you: "When It Starts to Start It'll Never Stop" (Magnapop)
>
>
> On Wed, Dec 20, 2017 at 2:20 PM, Alex  wrote:
>
>> The description for the Urey-Bradley potential (assuming two quadratic
>> terms qualify for the proud term "potential") is described in the user
>> manual, and the constants' order of appearance in the itp file is given in
>> the Table 5.5 of the manual. If you have a basic quadratic angular term
>> (first term in U-B with two constants) from elsewhere and you want to use
>> it in the U-B format, it is an absolutely trivial task. All you have to do
>> is set the U-B distance-dependent energy component to zero.
>>
>> Alex
>>
>>
>>
>> On 12/20/2017 12:05 AM, RAHUL SURESH wrote:
>>
>>> Hi
>>>
>>> Thank you Mark.
>>>
>>> On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham >> >
>>> wrote:
>>>
>>> Hi,

 Sorry I don't know how any of these non-GROMACS tools work, or even
 whether
 they actually generate Urey Bradley interactions that have all the
 terms. I
 suggest you spend some time with the documentation.

 Mark

 On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH 
 wrote:

 Sorry Mark, I failed to note that.
>
> I am afraid that I don't know what that are those components and how
> and
> where to find it. If you are actually meaning about "ub0 kub"
>
 components,

> how could i find the value for it. In case of swiss param generated itp
> file, these components appear to be 0. Any help here please?
>
>
> On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham <
> mark.j.abra...@gmail.com
>
> wrote:
>
> Hi,
>>
>> Please read my answer.
>>
>> Mark
>>
>> On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH 
>> wrote:
>>
>> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul 
>>>
>> wrote:

>
 On 12/19/17 11:14 AM, RAHUL SURESH wrote:

> Dear all
>
> For grompp em.mdp I get an error
>
> ERROR 1 [file THC.itp, line 89]:
> Incorrect number of parameters - found 2, expected 4 or 8 for
>
 U-B.
>
>> My itp file as follows
>
> [ angles ]
>
> 1   2   29   579.178   109.588 *{Line 89}*
> 1   2   3 532.192   112.817
> 2   3   31   551.424   109.189
>
>   From the manual chapter 5, function of U-B is 5. And it works
>
 fine

> for
>>
>>> function type 2 and 8.
>
> Any thing better could be done?
>
 As the error tells you, the U-B functional form requires at least 4
 parameters; look at its functional form. See Table 5.5.

>>>
>>> Dear Justin
>>>
>>> But the parameter obtained from ffTK have only two. What could be
>>>
>> done.?
>
>>
 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Assistant Professor
 Virginia Tech Department of Biochemistry

 303 Engel Hall
 340 West Campus Dr.
 Blacksburg, VA 24061

 jalem...@vt.edu | (540) 231-3129
 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

 ==

Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-20 Thread RAHUL SURESH

Dear Alex

I have tried that but the system collapse. For em_real.mdp option,I get
message stating

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.1#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  3.9192084e+11
Maximum force =  1.3457252e+14 on atom 629
Norm of force =  1.0629695e+12

Simulation ended prematurely, no performance report will be written.

GROMACS reminds you: "When It Starts to Start It'll Never Stop" (Magnapop)

On Wed, Dec 20, 2017 at 2:20 PM, Alex  wrote:

> The description for the Urey-Bradley potential (assuming two quadratic
> terms qualify for the proud term "potential") is described in the user
> manual, and the constants' order of appearance in the itp file is given in
> the Table 5.5 of the manual. If you have a basic quadratic angular term
> (first term in U-B with two constants) from elsewhere and you want to use
> it in the U-B format, it is an absolutely trivial task. All you have to do
> is set the U-B distance-dependent energy component to zero.
>
> Alex
>
>
>
> On 12/20/2017 12:05 AM, RAHUL SURESH wrote:
>
>> Hi
>>
>> Thank you Mark.
>>
>> On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> Sorry I don't know how any of these non-GROMACS tools work, or even
>>> whether
>>> they actually generate Urey Bradley interactions that have all the
>>> terms. I
>>> suggest you spend some time with the documentation.
>>>
>>> Mark
>>>
>>> On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH 
>>> wrote:
>>>
>>> Sorry Mark, I failed to note that.

 I am afraid that I don't know what that are those components and how and
 where to find it. If you are actually meaning about "ub0 kub"

>>> components,
>>>
 how could i find the value for it. In case of swiss param generated itp
 file, these components appear to be 0. Any help here please?

 On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham <
 mark.j.abra...@gmail.com

 wrote:

 Hi,
>
> Please read my answer.
>
> Mark
>
> On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH 
> wrote:
>
> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul 
>>
> wrote:
>>>

>>> On 12/19/17 11:14 AM, RAHUL SURESH wrote:
>>>
 Dear all

 For grompp em.mdp I get an error

 ERROR 1 [file THC.itp, line 89]:
 Incorrect number of parameters - found 2, expected 4 or 8 for

>>> U-B.

> My itp file as follows

 [ angles ]

 1   2   29   579.178   109.588 *{Line 89}*
 1   2   3 532.192   112.817
 2   3   31   551.424   109.189

   From the manual chapter 5, function of U-B is 5. And it works

>>> fine
>>>
 for
>
>> function type 2 and 8.

 Any thing better could be done?

>>> As the error tells you, the U-B functional form requires at least 4
>>> parameters; look at its functional form. See Table 5.5.
>>>
>>
>> Dear Justin
>>
>> But the parameter obtained from ffTK have only two. What could be
>>
> done.?

>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>
>> or

> send a mail

Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-20 Thread Alex

The description for the Urey-Bradley potential (assuming two quadratic 
terms qualify for the proud term "potential") is described in the user 
manual, and the constants' order of appearance in the itp file is given 
in the Table 5.5 of the manual. If you have a basic quadratic angular 
term (first term in U-B with two constants) from elsewhere and you want 
to use it in the U-B format, it is an absolutely trivial task. All you 
have to do is set the U-B distance-dependent energy component to zero.


Alex


On 12/20/2017 12:05 AM, RAHUL SURESH wrote:

Hi

Thank you Mark.

On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham 
wrote:


Hi,

Sorry I don't know how any of these non-GROMACS tools work, or even whether
they actually generate Urey Bradley interactions that have all the terms. I
suggest you spend some time with the documentation.

Mark

On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH 
wrote:


Sorry Mark, I failed to note that.

I am afraid that I don't know what that are those components and how and
where to find it. If you are actually meaning about "ub0 kub"

components,

how could i find the value for it. In case of swiss param generated itp
file, these components appear to be 0. Any help here please?


On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham 
wrote:


On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul 

wrote:


On 12/19/17 11:14 AM, RAHUL SURESH wrote:

Dear all

For grompp em.mdp I get an error

ERROR 1 [file THC.itp, line 89]:
Incorrect number of parameters - found 2, expected 4 or 8 for

U-B.

My itp file as follows

[ angles ]

1   2   29   579.178   109.588 *{Line 89}*
1   2   3 532.192   112.817
2   3   31   551.424   109.189

  From the manual chapter 5, function of U-B is 5. And it works

fine

for

function type 2 and 8.

Any thing better could be done?

As the error tells you, the U-B functional form requires at least 4
parameters; look at its functional form. See Table 5.5.


Dear Justin

But the parameter obtained from ffTK have only two. What could be

done.?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-19 Thread RAHUL SURESH

Hi

Thank you Mark.

On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham 
wrote:

> Hi,
>
> Sorry I don't know how any of these non-GROMACS tools work, or even whether
> they actually generate Urey Bradley interactions that have all the terms. I
> suggest you spend some time with the documentation.
>
> Mark
>
> On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH 
> wrote:
>
> > Sorry Mark, I failed to note that.
> >
> > I am afraid that I don't know what that are those components and how and
> > where to find it. If you are actually meaning about "ub0 kub"
> components,
> > how could i find the value for it. In case of swiss param generated itp
> > file, these components appear to be 0. Any help here please?
> >
> >
> > On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham  >
> > wrote:
> >
> > > Hi,
> > >
> > > Please read my answer.
> > >
> > > Mark
> > >
> > > On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH 
> > > wrote:
> > >
> > > > On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul 
> wrote:
> > > >
> > > > >
> > > > >
> > > > > On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > > > > > Dear all
> > > > > >
> > > > > > For grompp em.mdp I get an error
> > > > > >
> > > > > > ERROR 1 [file THC.itp, line 89]:
> > > > > >Incorrect number of parameters - found 2, expected 4 or 8 for
> > U-B.
> > > > > >
> > > > > > My itp file as follows
> > > > > >
> > > > > > [ angles ]
> > > > > >
> > > > > > 1   2   29   579.178   109.588 *{Line 89}*
> > > > > > 1   2   3 532.192   112.817
> > > > > > 2   3   31   551.424   109.189
> > > > > >
> > > > > >  From the manual chapter 5, function of U-B is 5. And it works
> fine
> > > for
> > > > > > function type 2 and 8.
> > > > > >
> > > > > > Any thing better could be done?
> > > > >
> > > > > As the error tells you, the U-B functional form requires at least 4
> > > > > parameters; look at its functional form. See Table 5.5.
> > > >
> > > >
> > > > Dear Justin
> > > >
> > > > But the parameter obtained from ffTK have only two. What could be
> > done.?
> > > >
> > > > >
> > > > >
> > > > > -Justin
> > > > >
> > > > > --
> > > > > ==
> > > > >
> > > > > Justin A. Lemkul, Ph.D.
> > > > > Assistant Professor
> > > > > Virginia Tech Department of Biochemistry
> > > > >
> > > > > 303 Engel Hall
> > > > > 340 West Campus Dr.
> > > > > Blacksburg, VA 24061
> > > > >
> > > > > jalem...@vt.edu | (540) 231-3129
> > > > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > > > >
> > > > > ==
> > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
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> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > *Regards,*
> > > > *Rahul Suresh*
> > > > *Research Scholar*
> > > > *Bharathiar University*
> > > > *Coimbatore*
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> > >
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > Gromacs Users mailing list
> >
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Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-19 Thread Mark Abraham

Hi,

Sorry I don't know how any of these non-GROMACS tools work, or even whether
they actually generate Urey Bradley interactions that have all the terms. I
suggest you spend some time with the documentation.

Mark

On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH  wrote:

> Sorry Mark, I failed to note that.
>
> I am afraid that I don't know what that are those components and how and
> where to find it. If you are actually meaning about "ub0 kub"  components,
> how could i find the value for it. In case of swiss param generated itp
> file, these components appear to be 0. Any help here please?
>
>
> On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Please read my answer.
> >
> > Mark
> >
> > On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH 
> > wrote:
> >
> > > On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul  wrote:
> > >
> > > >
> > > >
> > > > On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > > > > Dear all
> > > > >
> > > > > For grompp em.mdp I get an error
> > > > >
> > > > > ERROR 1 [file THC.itp, line 89]:
> > > > >Incorrect number of parameters - found 2, expected 4 or 8 for
> U-B.
> > > > >
> > > > > My itp file as follows
> > > > >
> > > > > [ angles ]
> > > > >
> > > > > 1   2   29   579.178   109.588 *{Line 89}*
> > > > > 1   2   3 532.192   112.817
> > > > > 2   3   31   551.424   109.189
> > > > >
> > > > >  From the manual chapter 5, function of U-B is 5. And it works fine
> > for
> > > > > function type 2 and 8.
> > > > >
> > > > > Any thing better could be done?
> > > >
> > > > As the error tells you, the U-B functional form requires at least 4
> > > > parameters; look at its functional form. See Table 5.5.
> > >
> > >
> > > Dear Justin
> > >
> > > But the parameter obtained from ffTK have only two. What could be
> done.?
> > >
> > > >
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Assistant Professor
> > > > Virginia Tech Department of Biochemistry
> > > >
> > > > 303 Engel Hall
> > > > 340 West Campus Dr.
> > > > Blacksburg, VA 24061
> > > >
> > > > jalem...@vt.edu | (540) 231-3129
> > > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > > >
> > > > ==
> > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
> > > 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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> > --
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> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-19 Thread RAHUL SURESH

Sorry Mark, I failed to note that.

I am afraid that I don't know what that are those components and how and
where to find it. If you are actually meaning about "ub0 kub"  components,
how could i find the value for it. In case of swiss param generated itp
file, these components appear to be 0. Any help here please?


On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham 
wrote:

> Hi,
>
> Please read my answer.
>
> Mark
>
> On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH 
> wrote:
>
> > On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > > > Dear all
> > > >
> > > > For grompp em.mdp I get an error
> > > >
> > > > ERROR 1 [file THC.itp, line 89]:
> > > >Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
> > > >
> > > > My itp file as follows
> > > >
> > > > [ angles ]
> > > >
> > > > 1   2   29   579.178   109.588 *{Line 89}*
> > > > 1   2   3 532.192   112.817
> > > > 2   3   31   551.424   109.189
> > > >
> > > >  From the manual chapter 5, function of U-B is 5. And it works fine
> for
> > > > function type 2 and 8.
> > > >
> > > > Any thing better could be done?
> > >
> > > As the error tells you, the U-B functional form requires at least 4
> > > parameters; look at its functional form. See Table 5.5.
> >
> >
> > Dear Justin
> >
> > But the parameter obtained from ffTK have only two. What could be done.?
> >
> > >
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
> > > 303 Engel Hall
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalem...@vt.edu | (540) 231-3129
> > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >
> > > ==
> > >
> > > --
> > > 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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> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > 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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-19 Thread Mark Abraham

Hi,

Please read my answer.

Mark

On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH  wrote:

> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > > Dear all
> > >
> > > For grompp em.mdp I get an error
> > >
> > > ERROR 1 [file THC.itp, line 89]:
> > >Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
> > >
> > > My itp file as follows
> > >
> > > [ angles ]
> > >
> > > 1   2   29   579.178   109.588 *{Line 89}*
> > > 1   2   3 532.192   112.817
> > > 2   3   31   551.424   109.189
> > >
> > >  From the manual chapter 5, function of U-B is 5. And it works fine for
> > > function type 2 and 8.
> > >
> > > Any thing better could be done?
> >
> > As the error tells you, the U-B functional form requires at least 4
> > parameters; look at its functional form. See Table 5.5.
>
>
> Dear Justin
>
> But the parameter obtained from ffTK have only two. What could be done.?
>
> >
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
> >
> > --
> > 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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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-19 Thread RAHUL SURESH

On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul  wrote:

>
>
> On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > Dear all
> >
> > For grompp em.mdp I get an error
> >
> > ERROR 1 [file THC.itp, line 89]:
> >Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
> >
> > My itp file as follows
> >
> > [ angles ]
> >
> > 1   2   29   579.178   109.588 *{Line 89}*
> > 1   2   3 532.192   112.817
> > 2   3   31   551.424   109.189
> >
> >  From the manual chapter 5, function of U-B is 5. And it works fine for
> > function type 2 and 8.
> >
> > Any thing better could be done?
>
> As the error tells you, the U-B functional form requires at least 4
> parameters; look at its functional form. See Table 5.5.


Dear Justin

But the parameter obtained from ffTK have only two. What could be done.?

>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-19 Thread Mark Abraham

Hi,

The CHARMM software implements UB with two separate bond and angle
components, which you probably have to find and to insert here, to suit the
way GROMACS implements the interaction in a self-contained way.

Mark

On Wed, Dec 20, 2017, 10:36 AM Justin Lemkul  wrote:

>
>
> On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > Dear all
> >
> > For grompp em.mdp I get an error
> >
> > ERROR 1 [file THC.itp, line 89]:
> >Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
> >
> > My itp file as follows
> >
> > [ angles ]
> >
> > 1   2   29   579.178   109.588 *{Line 89}*
> > 1   2   3 532.192   112.817
> > 2   3   31   551.424   109.189
> >
> >  From the manual chapter 5, function of U-B is 5. And it works fine for
> > function type 2 and 8.
> >
> > Any thing better could be done?
>
> As the error tells you, the U-B functional form requires at least 4
> parameters; look at its functional form. See Table 5.5.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Grompp error : Incorrect number of parameters

2017-12-19 Thread Justin Lemkul




On 12/19/17 11:14 AM, RAHUL SURESH wrote:

Dear all

For grompp em.mdp I get an error

ERROR 1 [file THC.itp, line 89]:
   Incorrect number of parameters - found 2, expected 4 or 8 for U-B.

My itp file as follows

[ angles ]

1   2   29   579.178   109.588 *{Line 89}*
1   2   3 532.192   112.817
2   3   31   551.424   109.189

 From the manual chapter 5, function of U-B is 5. And it works fine for
function type 2 and 8.

Any thing better could be done?


As the error tells you, the U-B functional form requires at least 4 
parameters; look at its functional form. See Table 5.5.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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[gmx-users] Grompp error : Incorrect number of parameters

2017-12-19 Thread RAHUL SURESH

Dear all

For grompp em.mdp I get an error

ERROR 1 [file THC.itp, line 89]:
  Incorrect number of parameters - found 2, expected 4 or 8 for U-B.

My itp file as follows

[ angles ]

1   2   29   579.178   109.588 *{Line 89}*
1   2   3 532.192   112.817
2   3   31   551.424   109.189

>From the manual chapter 5, function of U-B is 5. And it works fine for
function type 2 and 8.

Any thing better could be done?

*PS: The itp file is constructed from parameter file of ffTK.*

Thank you


-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*

*India*
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[gmx-users] Grompp error : Incorrect number of parameters

2017-12-18 Thread RAHUL SURESH

Dear all

For grompp em.mdp I get an error

ERROR 1 [file THC.itp, line 89]:
  Incorrect number of parameters - found 2, expected 4 or 8 for U-B.

My itp file as follows

[ angles ]

1   2   29   579.178   109.588 *{Line 89}*
1   2   3 532.192   112.817
2   3   31   551.424   109.189

>From the manual chapter 5, function of U-B is 5. And it works fine for
function type 2 and 8.

Any thing better could be done?

*PS: The itp file is constructed from parameter file of ffTK.*

Thank you


-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] grompp error

2017-10-16 Thread Dallas Warren

My guess would be that when you thought ran it with the increased box
size coordinate file, you actually used the original coordinate file.

FYI 
http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 16 October 2017 at 12:22, Amali Guruge  wrote:
> Dear Gromacs users,
>
> I got the following error when I tried to run grompp.
> ERROR 1 [file system.top, line 18]:
>   ERROR: One of the box lengths is smaller than twice the cut-off length.
>   Increase the box size or decrease rlist
>
> I increased the box size and re-tried to run grompp,but it didn't work. The
> box size is 20*20*20 nm3. mdp file options are shown in below. Could you
> please anyone help me to solve this problem.
>
> Thank you.
>
> ; Define can be used to control processes
> define  = -DFLEXIBLE
>
> ; Parameters describing what to do, when to stop and what to save
> integrator= steep; Algorithm (steep = steepest descent
> minimization)
> emtol= 1.0; Stop minimization when the maximum force < 1.0
> kJ/mol
> nsteps= 200; Maximum number of (minimization) steps to
> perform
> nstenergy= 10; Write energies to disk every nstenergy steps
> nstcalcenergy= 10; Calculate energy every step
> energygrps= System; Which energy group(s) to write to disk
> nstxout   = 100  ; Frequency of writing to .trr file
>
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> cutoff-scheme   = Verlet
> ns_type= simple; Method to determine neighbor list (simple,
> grid)
> coulombtype= cut-off; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.0; long range electrostatic cut-off
> rvdw= 1.0; long range Van der Waals cut-off
> constraints= none; Bond types to replace by constraints
> pbc= xyz; Periodic Boundary Conditions (yes/no)
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[gmx-users] grompp error

2017-10-15 Thread Amali Guruge

Dear Gromacs users,

I got the following error when I tried to run grompp.
ERROR 1 [file system.top, line 18]:
  ERROR: One of the box lengths is smaller than twice the cut-off length.
  Increase the box size or decrease rlist

I increased the box size and re-tried to run grompp,but it didn't work. The
box size is 20*20*20 nm3. mdp file options are shown in below. Could you
please anyone help me to solve this problem.

Thank you.

; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 1.0; Stop minimization when the maximum force < 1.0
kJ/mol
nsteps= 200; Maximum number of (minimization) steps to
perform
nstenergy= 10; Write energies to disk every nstenergy steps
nstcalcenergy= 10; Calculate energy every step
energygrps= System; Which energy group(s) to write to disk
nstxout   = 100  ; Frequency of writing to .trr file


; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
cutoff-scheme   = Verlet
ns_type= simple; Method to determine neighbor list (simple,
grid)
coulombtype= cut-off; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; long range electrostatic cut-off
rvdw= 1.0; long range Van der Waals cut-off
constraints= none; Bond types to replace by constraints
pbc= xyz; Periodic Boundary Conditions (yes/no)
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Re: [gmx-users] Grompp error for graphene modeling

2017-05-28 Thread ‪Mohammad Roostaie‬ ‪

Thanks Justin for your help. I will modify the force field again to model the 
particles better.
Best,Mohammad

  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Saturday, 27 May 2017, 23:20:26
 Subject: Re: [gmx-users] Grompp error for graphene modeling

On 5/27/17 3:33 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi All,
> I modeled graphene in a box of water with a peptide in the center of the box. 
> I modified the OPLS-AA force field by adding the parameters from this link to 
> the modified force field: http://chembytes.wikidot.com/grocnt. But, when I 
> want to add ions to the system, I got this warning:
> WARNING 1 [file ffbonded.itp, line 305]:  Overriding Bond parameters.
>    old:                                          0.151 292880 0.151 292880  
>new: C    C      1    0.14000  392459.2
> Actually, in the ffbonded.itp file, I put two parameters for C-C which the 
> new one referes to the graphene, and, I cannot change the names in the itp 
> file since the graphene atom names are C.Is this an important warning (May it 
> affect the stability of the system and results)? Or may I use -maxwarn?

Atom *names* and *types* are different beasts.  Types are used in 
ffnonbonded.itp and applied to the atoms found in the topology.  Atom names are 
irrelevant for parameter assignment.  But here you have introduced clearly 
conflicting parameters that will alter the behavior of the conflicting types, 
e.g. any aromatic rings in your peptide will behave incorrectly if you proceed 
with what you're doing.

In general, do not use -maxwarn unless you can clearly articulate why you're 
overriding a serious warning from grompp, not simply to make a problem go away.

-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] Grompp error for graphene modeling

2017-05-27 Thread Justin Lemkul




On 5/27/17 3:33 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Hi All,
I modeled graphene in a box of water with a peptide in the center of the box. I 
modified the OPLS-AA force field by adding the parameters from this link to the 
modified force field: http://chembytes.wikidot.com/grocnt. But, when I want to 
add ions to the system, I got this warning:
WARNING 1 [file ffbonded.itp, line 305]:  Overriding Bond parameters.
   old:  0.151 292880 0.151 292880  
new: C C   10.14000   392459.2
Actually, in the ffbonded.itp file, I put two parameters for C-C which the new 
one referes to the graphene, and, I cannot change the names in the itp file 
since the graphene atom names are C.Is this an important warning (May it affect 
the stability of the system and results)? Or may I use -maxwarn?


Atom *names* and *types* are different beasts.  Types are used in 
ffnonbonded.itp and applied to the atoms found in the topology.  Atom names are 
irrelevant for parameter assignment.  But here you have introduced clearly 
conflicting parameters that will alter the behavior of the conflicting types, 
e.g. any aromatic rings in your peptide will behave incorrectly if you proceed 
with what you're doing.


In general, do not use -maxwarn unless you can clearly articulate why you're 
overriding a serious warning from grompp, not simply to make a problem go away.


-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] Grompp error for graphene modeling

2017-05-27 Thread ‪Mohammad Roostaie‬ ‪

Hi All,
I modeled graphene in a box of water with a peptide in the center of the box. I 
modified the OPLS-AA force field by adding the parameters from this link to the 
modified force field: http://chembytes.wikidot.com/grocnt. But, when I want to 
add ions to the system, I got this warning:
WARNING 1 [file ffbonded.itp, line 305]:  Overriding Bond parameters.
  old:                                          0.151 292880 0.151 292880  new: 
C     C       1    0.14000   392459.2
Actually, in the ffbonded.itp file, I put two parameters for C-C which the new 
one referes to the graphene, and, I cannot change the names in the itp file 
since the graphene atom names are C.Is this an important warning (May it affect 
the stability of the system and results)? Or may I use -maxwarn? 
Best,Mohammad

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[gmx-users] grompp error

2017-05-25 Thread ‪Mohammad Roostaie‬ ‪

Hi GROMACS users,


 
I want to simulate a graphene sheet, and I want to use OPLS-AA force field. So, 
I copied the forcefield in my directory and changed some the files in it 
(ffbonded.itp, ffnonbonded.itp, atomtype.atp, aminoacids.rtp, and 
atomname2type.n2t). I used the pdb2gmx command to create the first topology and 
coordinate files with the modified OPLS-AA forcefield, then I created a box and 
solvated it with water. But, when I wanted to add ions to the box by using “gmx 
grompp -f ions.mdp -c gr_solv.gro -p gr.top -o ions.tpr”, I got this error: 


NOTE 1 [file ions.mdp]:  With Verlet lists the optimal nstlist is >= 10, with 
GPUs >= 20. Note  that with the Verlet scheme, nstlist has no effect on the 
accuracy of  your simulation.
Setting the LD random seed to 209904318
WARNING 1 [file ffbonded.itp, line 305]:  Overriding Bond parameters.
  old:                                          0.151 292880 0.151 292880  new: 
C     C       1    0.14000   392459.2
Generated 36 of the 36 non-bonded parameter combinationsGenerating 1-4 
interactions: fudge = 0.5Generated 36 of the 36 1-4 parameter 
combinations
---Program gmx grompp, 
VERSION 5.1.4Source code file: 
/home/jemmyhu/work/software/gromacs/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c,
 line: 755
Fatal error:Syntax error - File forcefield.itp, line 18Last line read:'[ 
defaults ]'Invalid order for directive defaultsFor more information and tips 
for troubleshooting, please check the GROMACSwebsite at 
http://www.gromacs.org/Documentation/Errors

Can you please help me to solve this problem?
Thanks,Mohammad
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[gmx-users] grompp error (segmentation fault)in gromacs version 5.0.6

2016-08-09 Thread iamdsoumi

Hi,

I carry on md run on protein-dna complex using  AMBER99SB-ILDN force
field. Here I state my problem.

   gmx_mpi pdb2gmx -f em267.pdb -o em267_processed.gro -p topol.top
-water tip3p -ignh
  it compile successfully.

  gmx_mpi editconf -f em267_processed.gro -o em267_newbox.gro -c -d
1.0 -bt cubic
it compile successfully.

gmx_mpi solvate -cp newbox.gro -cs spc216.gro -p topol.top -o em267_solv.gro
it compile successfully.

gmx_mpi grompp -f em.mdp -c em267_solv.gro -p topol.top -o em267_ions.tpr

Here is the problem.

gromacs states

Ignoring obsolete mdp entry 'title'

NOTE 1 [file em.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 1779290498

WARNING 1 [file topol_DNA_chain_D.itp, line 5]:
  Too few gb parameters for type localhost.localdomain


Couldn't find topology match for atomtype localhost.localdomain
Segmentation fault (core dumped)

I always take back up of the trajectory file in my external hard disk and
delete the data from gpu.

What is the problem ?Problem even exists in  pdb which can be run foremerly
without any problem.Does anyone know how to solve this issue?

Thanks.
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[gmx-users] grompp error(Segmentation fault)in gromacs version 5.0.6

2016-08-05 Thread soumi

Hi, I carry on md run on protein-dna complex using 
AMBER99SB-ILDN force field. Here I state my 
problem. gmx_mpi pdb2gmx -f em267.pdb -o 
em267_processed.gro -p topol.top -water tip3p 
-ignh it compile 
successfully. gmx_mpi 
editconf -f em267_processed.gro -o em267_newbox.gro -c -d 1.0 -bt 
cubic it compile successfully.gmx_mpi 
solvate -cp newbox.gro -cs spc216.gro -p topol.top -o em267_solv.groit compile 
successfully.gmx_mpi grompp -f em.mdp -c em267_solv.gro -p topol.top -o 
em267_ions.tprHere is the problem.gromacs statesIgnoring obsolete mdp entry 
titleNOTE 1 [file em.mdp]: With Verlet lists the optimal 
nstlist is = 10, with GPUs = 20. Note that with the Verlet 
scheme, nstlist has no effect on the accuracy of your simulation.Setting 
the LD random seed to 17792
 90498WARNING 1 [file topol_DNA_chain_D.itp, line 5]: Too few gb 
parameters for type localhost.localdomainCouldnt find topology match for 
atomtype localhost.localdomainSegmentation fault (core dumped)I always take 
back up of the trajectory file in my external hard disk and delete the data 
from gpu.What is the problem ?Problem even exists in pdb which can be run 
foremerly without any problem.Does anyone know how to solve this 
issue?Thanks.Soumi
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Re: [gmx-users] Grompp error

2016-05-30 Thread Anurag Dobhal

Thanks a lot for your insight.

I will redefine them.




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Mon, May 30, 2016 at 8:26 PM, Justin Lemkul  wrote:

>
>
> On 5/30/16 10:55 AM, Anurag Dobhal wrote:
>
>> Thanks a lot for your reply.
>>
>> I have set tc-groups as
>>
>>
>> tc-grps = Other   acetone ; two coupling groups - more accurate
>> tau_t = 0.1  0.1   ; time constant, in ps
>> ref_t = 300  300   ; reference temperature, one for each
>>
>>
>>
> Then you can't rely on such groups to be correct.  Other and acetone
> overlap. Define appropriate groups.
>
> -Justin
>
>
>>
>> *Anurag Dobhal*
>> *Graduate Student (Bioprocess Technology)*
>> *Institute of Chemical Technology, Mumbai*
>> *Contact: +91 8898486877*
>>
>>
>>
>> On Mon, May 30, 2016 at 8:18 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/30/16 10:40 AM, Anurag Dobhal wrote:
>>>
>>> Dear Gromacs users

 I am solvating my molecule ( a ploymer chain, having 78 atoms) in
 Propan-2-one
 [ molecules] = acetone. I have already updated  [ molecules ] section in
 the topology file (topol.top) after the solvation step.

 after the sucessful energy minimization step, while runing grompp I am
 geting an error,

 " Excluding 3 bonded neighbours molecule type 'Other'
 turning all bonds into constraints...
 Excluding 3 bonded neighbours molecule type 'acetone'
 turning all bonds into constraints...
 Setting gen_seed to 3080450167
 Velocities were taken from a Maxwell distribution at 300 K
 Removing all charge groups because cutoff-scheme=Verlet

 Fatal error:
 Atom 79 in multiple T-Coupling groups (1 and 2) "

 The error means that T-coupling is treating both the polymer (other) and
 solvent (acetone) as other molecules.
 How can I rectify the error ?


 You haven't shown us what you've set as tc-grps but there is clearly
>>> redundancy between whatever those groups are.  If you have multiple
>>> groups,
>>> you need to ensure that they are defined correctly, using index groups as
>>> needed.
>>>
>>> -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
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
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>>>
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> 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] Grompp error

2016-05-30 Thread Anurag Dobhal

Thanks a lot for your reply.

I have set tc-groups as


tc-grps = Other   acetone ; two coupling groups - more accurate
tau_t = 0.1  0.1   ; time constant, in ps
ref_t = 300  300   ; reference temperature, one for each




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Mon, May 30, 2016 at 8:18 PM, Justin Lemkul  wrote:

>
>
> On 5/30/16 10:40 AM, Anurag Dobhal wrote:
>
>> Dear Gromacs users
>>
>> I am solvating my molecule ( a ploymer chain, having 78 atoms) in
>> Propan-2-one
>> [ molecules] = acetone. I have already updated  [ molecules ] section in
>> the topology file (topol.top) after the solvation step.
>>
>> after the sucessful energy minimization step, while runing grompp I am
>> geting an error,
>>
>> " Excluding 3 bonded neighbours molecule type 'Other'
>> turning all bonds into constraints...
>> Excluding 3 bonded neighbours molecule type 'acetone'
>> turning all bonds into constraints...
>> Setting gen_seed to 3080450167
>> Velocities were taken from a Maxwell distribution at 300 K
>> Removing all charge groups because cutoff-scheme=Verlet
>>
>> Fatal error:
>> Atom 79 in multiple T-Coupling groups (1 and 2) "
>>
>> The error means that T-coupling is treating both the polymer (other) and
>> solvent (acetone) as other molecules.
>> How can I rectify the error ?
>>
>>
> You haven't shown us what you've set as tc-grps but there is clearly
> redundancy between whatever those groups are.  If you have multiple groups,
> you need to ensure that they are defined correctly, using index groups as
> needed.
>
> -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
>
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> http://mackerell.umaryland.edu/~jalemkul
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Re: [gmx-users] Grompp error

2016-05-30 Thread Justin Lemkul




On 5/30/16 10:40 AM, Anurag Dobhal wrote:

Dear Gromacs users

I am solvating my molecule ( a ploymer chain, having 78 atoms) in Propan-2-one
[ molecules] = acetone. I have already updated  [ molecules ] section in
the topology file (topol.top) after the solvation step.

after the sucessful energy minimization step, while runing grompp I am
geting an error,

" Excluding 3 bonded neighbours molecule type 'Other'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'acetone'
turning all bonds into constraints...
Setting gen_seed to 3080450167
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet

Fatal error:
Atom 79 in multiple T-Coupling groups (1 and 2) "

The error means that T-coupling is treating both the polymer (other) and
solvent (acetone) as other molecules.
How can I rectify the error ?



You haven't shown us what you've set as tc-grps but there is clearly redundancy 
between whatever those groups are.  If you have multiple groups, you need to 
ensure that they are defined correctly, using index groups as needed.


-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] Grompp error

2016-05-30 Thread Anurag Dobhal

Dear Gromacs users

I am solvating my molecule ( a ploymer chain, having 78 atoms) in Propan-2-one
[ molecules] = acetone. I have already updated  [ molecules ] section in
the topology file (topol.top) after the solvation step.

after the sucessful energy minimization step, while runing grompp I am
geting an error,

" Excluding 3 bonded neighbours molecule type 'Other'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'acetone'
turning all bonds into constraints...
Setting gen_seed to 3080450167
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet

Fatal error:
Atom 79 in multiple T-Coupling groups (1 and 2) "

The error means that T-coupling is treating both the polymer (other) and
solvent (acetone) as other molecules.
How can I rectify the error ?


*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*

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Re: [gmx-users] grompp error

2015-11-10 Thread محمد گره گشا

All Deadr

Hi

we want to run a protein-ligand MD simulation, when we use mdrun (mdrun -s
em.tpr -nt 4 -o em.trr -c complexpr.gro -e em.edr) we have not any error
but the run written killed:

Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps = 400
Killed
can anyone help please?

thanks

On Sun, Oct 18, 2015 at 10:36 AM, محمد گره گشا 
wrote:

> All dears
>
>
> we doing MD by oplsa ff for protein-ligand complex that we take from
> Autodock. we do this steps to add ligand as a residue at residue database,
> but when run grompp we face this error
>
> ERROR 1 [ file LIG.itp, line 401 ]:
>
>No default proper Dih. types
>
> Fatal error:
>
> There was 1 error in input file(s)
>
>
>
> can you help we please?
>
> so thank you.
>
> We attached LIG.itp
>
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Re: [gmx-users] grompp error

2015-11-10 Thread Mark Abraham

Hi,

That's happening somewhere outside GROMACS. Talk to your sysadmins.

Mark

‪On Tue, Nov 10, 2015 at 9:17 AM ‫محمد گره گشا‬‎ 
wrote:‬

> All Deadr
>
> Hi
>
> we want to run a protein-ligand MD simulation, when we use mdrun (mdrun -s
> em.tpr -nt 4 -o em.trr -c complexpr.gro -e em.edr) we have not any error
> but the run written killed:
>
> Steepest Descents:
> Tolerance (Fmax) = 1.0e+03
> Number of steps = 400
> Killed
> can anyone help please?
>
> thanks
>
> On Sun, Oct 18, 2015 at 10:36 AM, محمد گره گشا 
> wrote:
>
> > All dears
> >
> >
> > we doing MD by oplsa ff for protein-ligand complex that we take from
> > Autodock. we do this steps to add ligand as a residue at residue
> database,
> > but when run grompp we face this error
> >
> > ERROR 1 [ file LIG.itp, line 401 ]:
> >
> >No default proper Dih. types
> >
> > Fatal error:
> >
> > There was 1 error in input file(s)
> >
> >
> >
> > can you help we please?
> >
> > so thank you.
> >
> > We attached LIG.itp
> >
> --
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Re: [gmx-users] grompp error

2015-10-19 Thread Justin Lemkul




On 10/18/15 3:15 AM, محمد گره گشا wrote:

All dears

we run MD for protein-ligand complex that we take from Autodock. but when
we run grompp we face this error:

ERROR 1 [ file LIG.itp, line 401 ]
  No default Proper Dih. types

Fatal error:
There was 1 error in input file(s)
can any 1 help we to resolve this error pleas?



Look at line 401, identify those atom types, and parametrize the dihedral 
properly.  The error indicates the force field does not support the interaction 
you need.



we attached LIG.itp



This list does not accept attachments.

-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
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[gmx-users] grompp error

2015-10-18 Thread محمد گره گشا

All dears


we doing MD by oplsa ff for protein-ligand complex that we take from
Autodock. we do this steps to add ligand as a residue at residue database,
but when run grompp we face this error

ERROR 1 [ file LIG.itp, line 401 ]:

   No default proper Dih. types

Fatal error:

There was 1 error in input file(s)



can you help we please?

so thank you.

We attached LIG.itp
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[gmx-users] grompp error

2015-10-18 Thread محمد گره گشا

All dears


we doing MD by oplsa ff for protein-ligand complex that we take from
Autodock. we do this steps to add ligand as a residue at residue database,
but when run grompp we face this error

ERROR 1 [ file LIG.itp, line 401 ]:

   No default proper Dih. types

Fatal error:

There was 1 error in input file(s)



can you help we please?

so thank you.

We attached LIG.itp
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[gmx-users] grompp error

2015-10-18 Thread محمد گره گشا

All dears

we run MD for protein-ligand complex that we take from Autodock. but when
we run grompp we face this error:

ERROR 1 [ file LIG.itp, line 401 ]
 No default Proper Dih. types

Fatal error:
There was 1 error in input file(s)
can any 1 help we to resolve this error pleas?

we attached LIG.itp
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Re: [gmx-users] grompp error

2015-09-14 Thread Justin Lemkul




On 9/14/15 4:30 AM, faride badalkhani wrote:

Dear GROMACS users,

I need to simulate a hyper branched polymer (a polyamidoamine dendrimer). I
used the GROMOS53A6 to perform the simulation. But, I have a problem with
defining the angles and dihedrals that are between two residues (because of
dendrimers hyper branched structure). I can perform pdb2gmx and solvation,
but When I run grompp, I got this error " No default Proper Dih. types",


So here the force field doesn't support whatever dihedral(s) that grompp finds.


and ''Duplicate atom index (...) in dihedrals''. How should I figure it
out?



Here your topology is set up incorrectly, as the same atom is repeated in a 
given dihedral definition.


-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] grompp error

2015-09-14 Thread faride badalkhani

Dear GROMACS users,

I need to simulate a hyper branched polymer (a polyamidoamine dendrimer). I
used the GROMOS53A6 to perform the simulation. But, I have a problem with
defining the angles and dihedrals that are between two residues (because of
dendrimers hyper branched structure). I can perform pdb2gmx and solvation,
but When I run grompp, I got this error " No default Proper Dih. types",
and ''Duplicate atom index (...) in dihedrals''. How should I figure it
out?

I have shared all the files via

https://www.dropbox.com/s/dt4qcnksxpsv5ld/ca.zip?dl=0

sincerely,
Farideh
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[gmx-users] Grompp Error No default Ryckaert-Bell. types

2015-07-10 Thread Anurag Dobhal

Dear gromacs users.

I am simulating a molecule in opls-aa force field.
While running energy minimization I did get the error
No default Ryckaert-Bell. types.

I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO)
has No default Ryckaert-Bell. types. but on checking   ffbonded.itp I found
that this dihedral is already  present
as in line 1346 as.
  C  CT OH HO  3 -0.44350   3.83255   0.72801  -4.11705
  0.0   0.0 ;

anybody have any idea what is the reason for this error ???









*Anurag DobhalJunior Research fellowSupervisor: Dr. Ratnesh D.
JainDepartment of chemical engineeringInstitute of Chemical
Technology400019, +91 8898486877*

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Re: [gmx-users] Grompp Error No default Ryckaert-Bell. types

2015-07-10 Thread Justin Lemkul




On 7/10/15 9:47 AM, Anurag Dobhal wrote:

Dear gromacs users.

I am simulating a molecule in opls-aa force field.
While running energy minimization I did get the error
No default Ryckaert-Bell. types.

I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO)
has No default Ryckaert-Bell. types. but on checking   ffbonded.itp I found
that this dihedral is already  present
as in line 1346 as.
   C  CT OH HO  3 -0.44350   3.83255   0.72801  -4.11705
   0.0   0.0 ;

anybody have any idea what is the reason for this error ???



grompp doesn't lie.  Make sure you're looking at the right line/interaction in 
the topology.


-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] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Anurag Dobhal

Hello all

How can I address the No default Ryckaert-Bell. types error.
The error is also in between the atoms which are not bonded with each other.

Thank you

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Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Sasha

You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever.

Alex

Thank you for your reply.

I am simulating a PLGA (poly lactic co-glycolic acid molecle).
I get the topology file and I solvated the molecule.
my system is neutral.
while running the grompp I got 6 No default Ryckaert-Bell. types.

I rechecked my parameters in .rtp file and I found them correct, or may be I am unable to found the problem.

I am using ions.mdp file which is given in the tutorial (lysozyme tutorial).

I have attatched the .pdb file and the .rtp parameters for them.

can you please check the parameters which I have given. so that I can rectify the errors.

awaiting for your reply.

Best

Anurag Dobhal
Juniour Research fellow
Supervisor: Dr. Ratnesh D. Jain
Department of chemical engineering
Insttute of Chemical Technology
400019, +91 8898486877

On Mon, May 4, 2015 at 12:11 PM, Alex nedoma...@gmail.com wrote:

It may sound surprising, but this is resolved by either introducing
correct R-B term parameters in your topology/ff definitions, or by removing the mess from
the input coordinates, especially when non-bonded atoms are determined to
participate in a dihedral.

Humor aside, more information about the system is needed.

Alex

AD Hello all

AD How can I address the "No default Ryckaert-Bell. types error".
AD The error is also in between the atoms which are not bonded with each other.

AD Thank you

AD --

AD *DISCLAIMER:*

AD *This communication is intended only for the person or entity to which it
AD is addressed and may contain confidential and / or privileged material. Any
AD review, retransmission, dissemination or other use is prohibited. If you
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This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.

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Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Alex

"Which angles?" -- wait until Mark Abraham gets here.

You must have a very special version of aminoacids.rtp

Example: https://github.com/gromacs/gromacs/blob/master/share/top/gromos43a2.ff/aminoacids.rtp

Thank you

But which angles I need to add in .rtp file.

are you talking about impropers and dihedrals ???

as In aminoacid.rtp there is no section for angles.

Best

Anurag Dobhal
Juniour Research fellow
Supervisor: Dr. Ratnesh D. Jain
Department of chemical engineering
Insttute of Chemical Technology
400019, +91 8898486877

On Mon, May 4, 2015 at 12:47 PM, Sasha nedoma...@gmail.com wrote:

You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever.

Alex

Thank you for your reply.

I rechecked my parameters in .rtp file and I found them correct, or may be I am unable to found the problem.

I am using ions.mdp file which is given in the tutorial (lysozyme tutorial).

I have attatched the .pdb file and the .rtp parameters for them.

can you please check the parameters which I have given. so that I can rectify the errors.

awaiting for your reply.

Best

Anurag Dobhal
Juniour Research fellow
Supervisor: Dr. Ratnesh D. Jain
Department of chemical engineering
Insttute of Chemical Technology
400019, +91 8898486877

On Mon, May 4, 2015 at 12:11 PM, Alex nedoma...@gmail.com wrote:

Humor aside, more information about the system is needed.

Alex

AD Hello all

AD How can I address the "No default Ryckaert-Bell. types error".
AD The error is also in between the atoms which are not bonded with each other.

AD Thank you

AD --

AD *DISCLAIMER:*

--
Best regards,
Sasha mailto:nedoma...@gmail.com

--
Best regards,
Alex mailto:nedoma...@gmail.com

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Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Alex

The rtp file format and its acceptable entries are not forcefield-specific (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to give an example of that.
The oplsaa version of aminoacids.rtp only lists dihedral and improper angles explicitly, and that is exactly what's grompp complaining about in your case.

Alex

Dear Sir

I am using oplsaa force field.
In the .rtp file i did not found angles secion for any amino acid.
yes there are sections for dihedrals and impropers.

sorry for troubling you.

Best

Anurag Dobhal
Juniour Research fellow
Supervisor: Dr. Ratnesh D. Jain
Department of chemical engineering
Insttute of Chemical Technology
400019, +91 8898486877

On Mon, May 4, 2015 at 1:03 PM, Alex nedoma...@gmail.com wrote:

"Which angles?" -- wait until Mark Abraham gets here.

You must have a very special version of aminoacids.rtp

Example:https://github.com/gromacs/gromacs/blob/master/share/top/gromos43a2.ff/aminoacids.rtp

Thank you

But which angles I need to add in .rtp file.

are you talking about impropers and dihedrals ???

as In aminoacid.rtp there is no section for angles.

Best

Anurag Dobhal
Juniour Research fellow
Supervisor: Dr. Ratnesh D. Jain
Department of chemical engineering
Insttute of Chemical Technology
400019, +91 8898486877

On Mon, May 4, 2015 at 12:47 PM, Sasha nedoma...@gmail.com wrote:

You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever.

Alex

Thank you for your reply.

I rechecked my parameters in .rtp file and I found them correct, or may be I am unable to found the problem.

I am using ions.mdp file which is given in the tutorial (lysozyme tutorial).

I have attatched the .pdb file and the .rtp parameters for them.

can you please check the parameters which I have given. so that I can rectify the errors.

awaiting for your reply.

Best

Anurag Dobhal
Juniour Research fellow
Supervisor: Dr. Ratnesh D. Jain
Department of chemical engineering
Insttute of Chemical Technology
400019, +91 8898486877

On Mon, May 4, 2015 at 12:11 PM, Alex nedoma...@gmail.com wrote:

Humor aside, more information about the system is needed.

Alex

AD Hello all

AD How can I address the "No default Ryckaert-Bell. types error".
AD The error is also in between the atoms which are not bonded with each other.

AD Thank you

AD --

AD *DISCLAIMER:*

--
Best regards,
Sasha mailto:nedoma...@gmail.com

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Justin Lemkul




On 5/4/15 4:20 AM, Alex wrote:

The rtp file format and its acceptable entries are not forcefield-specific
(oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to
give an example of that.

The oplsaa version of aminoacids.rtp only lists dihedral and improper angles
explicitly, and that is exactly what's grompp complaining about in your case.



I seem to be only getting half of the messages in this conversation, but let me 
clear a few things up:


1. The errors about missing R-B parameters have nothing to do with missing 
angles in the .rtp.  R-B are dihedrals, so that's not what grompp is complaining 
about.
2. As far as bonded interactions are concerned, in the .rtp only [bonds] are 
required to define connectivity.  Remaining bonded interactions are then deduced 
from bond connectivity.  If a directive like [angles] or [dihedrals] is present, 
those values are used, instead.  If an [angles] directive is missing that just 
tells pdb2gmx create all possible angles from the given bonded connectivity.


-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] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Alex


JL 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are
JL required to define connectivity.  Remaining bonded interactions are then 
deduced
JL from bond connectivity.  If a directive like [angles] or [dihedrals] is 
present,
JL those values are used, instead.  If an [angles] directive is missing that 
just
JL tells pdb2gmx create all possible angles from the given bonded 
connectivity.

Well, yes, but the atomtypes were defined in that rtp and no correct
triplets or quadruplets were available in ffbonded for those
combinations. Then, either define directly
in rtp, or stick them into your ffbonded. Am I missing something here?

Alex

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Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Justin Lemkul




On 5/4/15 1:06 PM, Alex wrote:


JL 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are
JL required to define connectivity.  Remaining bonded interactions are then 
deduced
JL from bond connectivity.  If a directive like [angles] or [dihedrals] is 
present,
JL those values are used, instead.  If an [angles] directive is missing that 
just
JL tells pdb2gmx create all possible angles from the given bonded 
connectivity.

Well, yes, but the atomtypes were defined in that rtp and no correct
triplets or quadruplets were available in ffbonded for those
combinations. Then, either define directly
in rtp, or stick them into your ffbonded. Am I missing something here?



I was just clarifying what was a very (to me) confusing exchange.  The 
statements made could easily be taken out of context and misapplied.


oplsaa seems to look up triplets for [ angles ] elsewhere is not really right, 
that's what I was explaining about the fundamental way pdb2gmx processes the 
.rtp to write angles and dihedrals.


The oplsaa version of aminoacids.rtp only lists dihedral and improper angles 
explicitly, and that is exactly what's grompp complaining about in your case. 
As worded, this seems like you're saying that the fact that only dihedrals and 
impropers are listed is the source of the problem.  That's not the case, but 
what you say above is - the parameters for the defined interaction are simply 
not in the force field and therefore must be added.  Of course, if the OP had 
simply Googled the error, this information would have been readily apparent and 
would have saved all involved a lot of typing :)


-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] Grompp error No default Ryckaert-Bell. types

2015-05-04 Thread Alex

True, thats why i mentioned Mark.:-)  In all honesty, though, for small
molecules, i would prefer to ignore the new format and actually add
everything in the rtp entry to make ffbonded look like less of a zoo.
Also, it was late night of extreme gromacs intercourse for me, which
finally paid off. :-)

Alex
On May 4, 2015 11:31 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/4/15 1:06 PM, Alex wrote:


 JL 2. As far as bonded interactions are concerned, in the .rtp only
 [bonds] are
 JL required to define connectivity.  Remaining bonded interactions are
 then deduced
 JL from bond connectivity.  If a directive like [angles] or [dihedrals]
 is present,
 JL those values are used, instead.  If an [angles] directive is
 missing that just
 JL tells pdb2gmx create all possible angles from the given bonded
 connectivity.

 Well, yes, but the atomtypes were defined in that rtp and no correct
 triplets or quadruplets were available in ffbonded for those
 combinations. Then, either define directly
 in rtp, or stick them into your ffbonded. Am I missing something here?


 I was just clarifying what was a very (to me) confusing exchange.  The
 statements made could easily be taken out of context and misapplied.

 oplsaa seems to look up triplets for [ angles ] elsewhere is not really
 right, that's what I was explaining about the fundamental way pdb2gmx
 processes the .rtp to write angles and dihedrals.

 The oplsaa version of aminoacids.rtp only lists dihedral and improper
 angles explicitly, and that is exactly what's grompp complaining about in
 your case. As worded, this seems like you're saying that the fact that
 only dihedrals and impropers are listed is the source of the problem.
 That's not the case, but what you say above is - the parameters for the
 defined interaction are simply not in the force field and therefore must be
 added.  Of course, if the OP had simply Googled the error, this information
 would have been readily apparent and would have saved all involved a lot of
 typing :)

 -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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 posting!

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[gmx-users] grompp error - no molecules were defined in the system

2014-01-18 Thread rankinb

When running grompp, I am receiving the error No molecules were defined in
the system.  I have a relatively simple topology and .gro file.  I cannot
locate the source of the error.  Does anyone have any suggestions?  Here is
an example of the .gro and .top file that I am using.  Thanks.

HSb
1
1HSb S21   1.250   1.250   1.250
   2.5   2.5   2.5




[defaults]
;nbfunc comb-rule   gen-parsfudgeLJ fudgeQQ
1   1   yes 0.5 0.5

[atomtypes]
;name   bond_type   masscharge  ptype   C   A
HSb HSb 18.02   0   A   
0   0

[nonbond_params]
;i  j   funcC   A
HSb HSb 1   0   0

[ moleculetype ]

; Namenrexcl

HSb  3

[ atoms ]

;   nr   type  resnrresidueatom   cgnr   charge  
mass  typeBchargeB  massB
 1  HSb 1   HSbS2  1 0   18.02

 
[ system ]
HSb

[ molecules ]
HSb 1  

Blake Rankin
Purdue University 
Department of Chemistry
Ben-Amotz Lab
Research Assistant

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Re: [gmx-users] grompp error - no molecules were defined in the system

2014-01-18 Thread Justin Lemkul




On 1/18/14, 2:20 PM, rankinb wrote:

When running grompp, I am receiving the error No molecules were defined in
the system.  I have a relatively simple topology and .gro file.  I cannot
locate the source of the error.  Does anyone have any suggestions?  Here is
an example of the .gro and .top file that I am using.  Thanks.

HSb
 1
 1HSb S21   1.250   1.250   1.250
2.5   2.5   2.5




[defaults]
;nbfunc comb-rule   gen-parsfudgeLJ fudgeQQ
1   1   yes 0.5 0.5

[atomtypes]
;name   bond_type   masscharge  ptype   C   A
HSb HSb 18.02   0   A   
0   0

[nonbond_params]
;i  j   funcC   A
HSb HSb 1   0   0

[ moleculetype ]

; Namenrexcl

HSb  3

[ atoms ]

;   nr   type  resnrresidueatom   cgnr   charge
mass  typeBchargeB  massB
  1  HSb 1   HSbS2 1 0   18.02


[ system ]
HSb

[ molecules ]
HSb 1



Works fine for me.  Use dos2unix to get rid of any incorrect newline characters 
to see if that's it.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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