Thank you for your reply! I am not sure if this is the cause of the
problem, since the output looks the same for residues 2 to 10 and the
message is actually referring to Chloride Ions which are not part of the
residue. Do you know how to load the parameters for Cl- ?
On 03/27/2017 02:38 PM, Elvis Martis wrote:
> It seems the LCPO method does not have the parameters for those atoms hence it assigns carbon SA parameters to compute the SASA.
>
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in
> Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Andreas Tosstorff [mailto:andreas.tosstorff.cup.uni-muenchen.de]
> Sent: Monday, March 27, 2017 5:59 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] surf cpptraj non-standard residue
>
> Hi all,
>
>
> I stumbled across a problem analysing the trajectory of a peptide containing non-standard amino acids using the surf function in cpptraj.
> The non-standard residue is the first in the sequence (R1).
>
> These are the commands I used in cpptraj:
>
> parm DIM_solv.parm7
>
> trajin DIM_solv_prod.crd
>
> surf R1 :1 out sasa1.dat
>
> ...
>
> surf R10 :10 out sasa10.dat
>
> run
>
>
> The cpptraj output looks like this:
>
> ACTION SETUP FOR PARM 'DIM_solv.parm7' (10 actions):
> 0: [surf R1 :1 out sasa1.dat]
> LCPO surface area will be calculated for 14 atoms.
> 14 solute atoms.
> Warning: Using carbon SA parms for unknown atom 175 type Cl-
> Warning: Using carbon SA parms for unknown atom 350 type Cl-
> Warning: Using carbon SA parms for unknown atom 352 type Cl-
> Warning: Using carbon SA parms for unknown atom 353 type Cl-
>
> ...
>
>
>
> For R2 to R10 I the files sasa*.dat look fine, I receive one value per frame. However for sasa1.dat I get 10 values per frame:
>
> #Frame R
> 1 177.0622 140.8356 164.5719 57.5352 163.3728
> 122.6951136.7847 169.207108.0297 148.5364
>
> ...
>
> This is what desc R1 gives me in tleap:
>
>
> RESIDUE name: PCA
> RESIDUE sequence number: 1
> RESIDUE PDB sequence number: 1
> Type: undefined
> Connection atoms:
> Connect atom 1: A<C5 7>
> Improper torsions:
> Contents:
> A<H6 15>
> A<H5 14>
> A<H4 13>
> A<H3 12>
> A<H2 11>
> A<H1 10>
> A<O2 8>
> A<C5 7>
> A<O1 6>
> A<C4 5>
> A<C3 4>
> A<C2 3>
> A<C1 2>
> A<N1 1>
> >
>
> How can I get cpptraj to print the SASA for the entire residue? Is there something wrong with the parameter file?
> Thanks in advance for your help!
>
> Best,
> Andy
>
> --
> M.Sc. Andreas Tosstorff
> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie Department Pharmazie LMU München Butenandtstr. 5-13 ( Haus B)
> 81377 München
> Germany
> Tel.: +49 89 2180 77059
>
>
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> _______________________________________________
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--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Mon Mar 27 2017 - 06:00:06 PDT
