[gmx-users] Ethanolamine force-field parameters missing in charmm27.ff

[jneeraj]

Hello,

I plan to run a MD on a protein + ethanolamine (ETAM) system using Gromacs
ver 4.5.5 with charmm27 force-field. 
Though charmm27 force-field (top_all27_prot_lipid.inp, also see 
http://users.mccammon.ucsd.edu/~rlaw/top_all27_prot_lipid.inp.htm
  ) has
the force-field parameters for residue ETAM, charmm27.ff of gromacs does not
define ETAM residue. Is there any quick way of importing ETAM residue from
top_all27_prot_lipid.inp to charmm27.ff ?

Thank you,
Neeraj



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[gmx-users] g_rdf -surf -rdf res_com: details needed

[jneeraj]

Hello,
I wish to compute rdf of Na+ ions around protein surface. I use the command:
g_rdf -f traj.xtc -n index.ndx -o rdf_prot_Na_res_com.xvg -b 4 -s md.tpr
-surf mol -rdf res_com -bin 0.01

Since when -surf option is used, g_rdf does not normalize the rdf, I am
curious what does actually g_rdf reports in the output .xvg file? If we
refer to the Eq. (8.3) of gromacs_manual.pdf, which of the following value
gets reported in the output file:
1) \sum_{1,N_B} (\delta(r_{i,j}-r)) 
2) \sum_{1,N_B} (\delta(r_{i,j}-r)) / (4*pi*r^2)
3) \sum_{1,N_B} (\delta(r_{i,j}-r)) / (4*pi*r^2) / N_A

My hunch is that g_rdf -surf reports value calculated by Eq. 1 since
computing the term (4*pi*r^2) for an irregular surface is very complex.
Please advise ?

My second question is regarding the value of r_max. In the manual, it's
reported: Usually the value of rmax is half of the box length. When I
compute rdf using g_rdf -surf option, the value of maximum r is indeed half
the box length. However, I think the value of r_max, when -surf is used,
should be considerably less than the (box length)/2. If I am right, in this
case, r is the distance from the surface of the protein and not from the
center of the protein. Hence, r_max should be around the length of solvent
padding from protein surface. 

Thanks,
Neeraj


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[gmx-users] Re: Interchain Disulfide Bond

[jneeraj]

Thank you Mark for you prompt response. I tried:

$pdb2gmx -ignh -merge all -chainsep ter -ff amber99sb -water tip3p -f 
-o  -p  
$grompp -f  -c  -p  -o 

and it works perfectly, i.e. it correctly creates interchain disulfide bond.

However, when I use charmm27 force field instead of amber99sb, I get the
following error from grompp:

Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1346

Fatal error:
Unknown cmap torsion between atoms 3224 3226 3228 3234 3237


So I believe this error is specific to charmm27 force-field. Any thoughts ?

Thanks
neeraj

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[gmx-users] Interchain Disulfide Bond

[jneeraj]

Hello, 

I am trying to perform a MD simulation of a protein consisting of two
chains. These two chains are connected via single disulfide bond. 
These two chains are separated by TER record in the input pdb file. I am
using charmm27 force-field. The steps that I am following are: 

pdb2gmx –ignh –ss –chainsep ter –ff charmm27 –water tip3p -f  -o 
-p 

However this step DOES NOT generate interchain disulfide bond. So, I tried
to generate .top file using: 

pdb2gmx –ignh –ss –merge interactive –ff charmm27 –water tip3p -f  -o
 -p 
When asked for merging chains, I say "y" 

The above step generates correct disulfide bonds and termii; however when I
use 

grompp -f min_run.mdp -c  -p  –o 

I get the error: 
 
Program grompp, VERSION 4.5.5 
Source code file: toppush.c, line: 1346 

Fatal error: 
Unknown cmap torsion between atoms 3224 3226 3228 3234 3237 
 

These atoms are the chain 1 C-terminus and chain 2 N-terminus atoms. Hence,
physically this cmap torsion is not required. 

I will appreciate your suggestions in helping me resolve this issue. 

Thanks, 
Neeraj 

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[gmx-users] Interchain Disulfide Bond

[jneeraj]

Hello,

I am trying to perform a MD simulation of a protein consisting of two
chains. These two chains are connected via single disulfide bond.
These two chains are separated by TER record in the input pdb file. I am
using charmm27 force-field. The steps that I am following are:

pdb2gmx –ignh –ss –chainsep ter –ff charmm27 –water tip3p -f  -o 
-p 

However this step DOES NOT generate interchain disulfide bond. So, I tried
to generate .top file using:

pdb2gmx –ignh –ss –merge interactive –ff charmm27 –water tip3p -f  -o
 -p 
When asked for merging chains, I say "y"

The above step generates correct disulfide bonds and termii; however when I
use

grompp -f min_run.mdp -c solvate.gro -p VAK.top –o min1.tpr

I get the error:

Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1346

Fatal error:
Unknown cmap torsion between atoms 3224 3226 3228 3234 3237


These atoms are the chain 1 C-terminus and chain 2 N-terminus atoms. Hence,
physically this cmap torsion is not required. 

I will appreciate your suggestions in helping me resolve this issue.

Thanks,
Neeraj


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