[gmx-users] CMAP error

2010-12-09 Thread Jon Mujika 
Dear all,

I am setting up a system with GROMACS 4.5.3 and the CHARMM force
field. In the protein, I have a neutral lysine, for which CHARMM force
filed has a specific residue type (LSN). When I wrote LSN as residue
name in the initial pdb file, the topology file was perfectly created
by pdb2gmx. However, in the next step, grompp complained about the
CMAP torsion between the two previous residues:

Fatal error:
Unknown cmap torsion between atoms 2747 2749 2751 2754 2757

However, if the LYS residue was written in the initial pdb file and
the -lys option included with pdb2gmx (chosen the neutral protonation
state for this lysine), grompp did not complain.

The problem is that there is a deprotonated tyrosine (bound to a
metal) in my system. I created a new residue type, but again the
grompp complained about the CMAP between the two previous residues.
Unfortunately, in this case I can't fit the problem with any of the
pdb2gms options.
I think the problem arises when a non-standard residue is included in
the initial pdb file. Does someone else find this problem? I would
appreciate any advise about how to solve it.

Thanks in advance

Jon
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[gmx-users] CMAP error

2010-12-10 Thread Jon Mujika 
Dear Justin,

Thanks for your advice. You were wright. The problem was solved adding
the new residue name to residuetypes.dat

The issue was that when pdb2gmx found an unknown residue name, it
defined as "Others" system instead of "Protein". As a consequence,
the chain was capped there, adding a COO- termination to the "last"
residue of the protein.

Thanks again for the fast and efficient answer.

Jon

> I can't promise a solution, but you could try adding LSN and whatever other
> non-standard residues you need to use in residuetypes.dat.  I noticed that LSN
> is not there, which seems like an omission, since the other CHARMM-specific
> residue names are there.  When LYS is present, probably pdb2gmx is correctly
> interpreting the residue as protein before converting its name.  In the case 
> of
> LSN or any other non-standard residue, this may not be the case.  Check the
> output of pdb2gmx carefully for any messages that might indicate that a 
> residue
> of type "Other" was detected.  I've had this cause other problems.

> If adding LSN to residuetypes.dat fixes the problem, I will file a bugzilla.

> -Justin
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Re: [gmx-users] CMAP error

2010-12-09 Thread Justin A. Lemkul 



Jon Mujika wrote:

Dear all,

I am setting up a system with GROMACS 4.5.3 and the CHARMM force
field. In the protein, I have a neutral lysine, for which CHARMM force
filed has a specific residue type (LSN). When I wrote LSN as residue
name in the initial pdb file, the topology file was perfectly created
by pdb2gmx. However, in the next step, grompp complained about the
CMAP torsion between the two previous residues:

Fatal error:
Unknown cmap torsion between atoms 2747 2749 2751 2754 2757

However, if the LYS residue was written in the initial pdb file and
the -lys option included with pdb2gmx (chosen the neutral protonation
state for this lysine), grompp did not complain.

The problem is that there is a deprotonated tyrosine (bound to a
metal) in my system. I created a new residue type, but again the
grompp complained about the CMAP between the two previous residues.
Unfortunately, in this case I can't fit the problem with any of the
pdb2gms options.
I think the problem arises when a non-standard residue is included in
the initial pdb file. Does someone else find this problem? I would
appreciate any advise about how to solve it.



I can't promise a solution, but you could try adding LSN and whatever other 
non-standard residues you need to use in residuetypes.dat.  I noticed that LSN 
is not there, which seems like an omission, since the other CHARMM-specific 
residue names are there.  When LYS is present, probably pdb2gmx is correctly 
interpreting the residue as protein before converting its name.  In the case of 
LSN or any other non-standard residue, this may not be the case.  Check the 
output of pdb2gmx carefully for any messages that might indicate that a residue 
of type "Other" was detected.  I've had this cause other problems.


If adding LSN to residuetypes.dat fixes the problem, I will file a bugzilla.

-Justin


Thanks in advance

Jon


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] CMAP error

2010-12-09 Thread Amit Choubey 
This may not be related but it was not straight forward to do DPPC membrane
simulation using CHARMM FF in gromacs. The DPPC molecule was not defined at
all in the FF files.

The DPPC is defined in terms of two more residues in CHARMM.

amit

On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul  wrote:

>
>
> Jon Mujika wrote:
>
>> Dear all,
>>
>> I am setting up a system with GROMACS 4.5.3 and the CHARMM force
>> field. In the protein, I have a neutral lysine, for which CHARMM force
>> filed has a specific residue type (LSN). When I wrote LSN as residue
>> name in the initial pdb file, the topology file was perfectly created
>> by pdb2gmx. However, in the next step, grompp complained about the
>> CMAP torsion between the two previous residues:
>>
>> Fatal error:
>> Unknown cmap torsion between atoms 2747 2749 2751 2754 2757
>>
>> However, if the LYS residue was written in the initial pdb file and
>> the -lys option included with pdb2gmx (chosen the neutral protonation
>> state for this lysine), grompp did not complain.
>>
>> The problem is that there is a deprotonated tyrosine (bound to a
>> metal) in my system. I created a new residue type, but again the
>> grompp complained about the CMAP between the two previous residues.
>> Unfortunately, in this case I can't fit the problem with any of the
>> pdb2gms options.
>> I think the problem arises when a non-standard residue is included in
>> the initial pdb file. Does someone else find this problem? I would
>> appreciate any advise about how to solve it.
>>
>>
> I can't promise a solution, but you could try adding LSN and whatever other
> non-standard residues you need to use in residuetypes.dat.  I noticed that
> LSN is not there, which seems like an omission, since the other
> CHARMM-specific residue names are there.  When LYS is present, probably
> pdb2gmx is correctly interpreting the residue as protein before converting
> its name.  In the case of LSN or any other non-standard residue, this may
> not be the case.  Check the output of pdb2gmx carefully for any messages
> that might indicate that a residue of type "Other" was detected.  I've had
> this cause other problems.
>
> If adding LSN to residuetypes.dat fixes the problem, I will file a
> bugzilla.
>
> -Justin
>
>  Thanks in advance
>>
>> Jon
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] CMAP error

2010-12-09 Thread Thomas Piggot 
This is a completely separate issue where the CHARMM force field files 
from which the GROMACS CHARMM27 rtp entries were created do not have a 
DPPC entry, rather DPPC in CHARMM is created from using two residues 
(PALM and PCGL) and two patches (EST1 and EST2). It should have been 
easy enough to make a CHARMM27 DPPC rtp entry anyway.


Cheers

Tom

Amit Choubey wrote:
This may not be related but it was not straight forward to do DPPC 
membrane simulation using CHARMM FF in gromacs. The DPPC molecule was 
not defined at all in the FF files.


The DPPC is defined in terms of two more residues in CHARMM.

amit

On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul > wrote:




Jon Mujika wrote:

Dear all,

I am setting up a system with GROMACS 4.5.3 and the CHARMM force
field. In the protein, I have a neutral lysine, for which CHARMM
force
filed has a specific residue type (LSN). When I wrote LSN as residue
name in the initial pdb file, the topology file was perfectly
created
by pdb2gmx. However, in the next step, grompp complained about the
CMAP torsion between the two previous residues:

Fatal error:
Unknown cmap torsion between atoms 2747 2749 2751 2754 2757

However, if the LYS residue was written in the initial pdb file and
the -lys option included with pdb2gmx (chosen the neutral
protonation
state for this lysine), grompp did not complain.

The problem is that there is a deprotonated tyrosine (bound to a
metal) in my system. I created a new residue type, but again the
grompp complained about the CMAP between the two previous residues.
Unfortunately, in this case I can't fit the problem with any of the
pdb2gms options.
I think the problem arises when a non-standard residue is
included in
the initial pdb file. Does someone else find this problem? I would
appreciate any advise about how to solve it.


I can't promise a solution, but you could try adding LSN and
whatever other non-standard residues you need to use in
residuetypes.dat.  I noticed that LSN is not there, which seems like
an omission, since the other CHARMM-specific residue names are
there.  When LYS is present, probably pdb2gmx is correctly
interpreting the residue as protein before converting its name.  In
the case of LSN or any other non-standard residue, this may not be
the case.  Check the output of pdb2gmx carefully for any messages
that might indicate that a residue of type "Other" was detected.
 I've had this cause other problems.

If adding LSN to residuetypes.dat fixes the problem, I will file a
bugzilla.

-Justin

Thanks in advance

Jon


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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--
Dr Thomas Piggot
University of Southampton, UK.
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Re: [gmx-users] CMAP error

2010-12-10 Thread Justin A. Lemkul 



Jon Mujika wrote:

Dear Justin,

Thanks for your advice. You were wright. The problem was solved adding
the new residue name to residuetypes.dat

The issue was that when pdb2gmx found an unknown residue name, it
defined as "Others" system instead of "Protein". As a consequence,
the chain was capped there, adding a COO- termination to the "last"
residue of the protein.

Thanks again for the fast and efficient answer.



Bugzilla 621 filed.  Thanks for discovering this.

http://bugzilla.gromacs.org/show_bug.cgi?id=621

-Justin


Jon


I can't promise a solution, but you could try adding LSN and whatever other
non-standard residues you need to use in residuetypes.dat.  I noticed that LSN
is not there, which seems like an omission, since the other CHARMM-specific
residue names are there.  When LYS is present, probably pdb2gmx is correctly
interpreting the residue as protein before converting its name.  In the case of
LSN or any other non-standard residue, this may not be the case.  Check the
output of pdb2gmx carefully for any messages that might indicate that a residue
of type "Other" was detected.  I've had this cause other problems.



If adding LSN to residuetypes.dat fixes the problem, I will file a bugzilla.



-Justin


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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